Update Colvars to version 2020-07-07
This update contains several fixes and small new features or usability improvements. Descriptions and authorship information can be accessed from the pull requests listed below. Skip the zero-step also when multiple run commands are executed in sequence (@giacomofiorin) https://github.com/Colvars/colvars/pull/357 Do not accumulate data at step 0 (@giacomofiorin) https://github.com/Colvars/colvars/pull/345 Support for symmetry permutations of atoms in RMSD (@jhenin) https://github.com/Colvars/colvars/pull/344 Detect new grid parameters (@jhenin) https://github.com/Colvars/colvars/pull/341 Only access the output streams in non-threaded regions (@giacomofiorin) https://github.com/Colvars/colvars/pull/338 Fix incomplete setting of default colvarsRestartFrequency (@giacomofiorin) https://github.com/Colvars/colvars/pull/334 Fix typo (@e-kwsm) https://github.com/Colvars/colvars/pull/333 Convert the input keyword to lowercase in read_state_data_key (@HanatoK) https://github.com/Colvars/colvars/pull/332 Implement reflecting b.c. for ext Lagrangian (@jhenin) https://github.com/Colvars/colvars/pull/329
This commit is contained in:
Giacomo Fiorin
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@ -38,6 +38,7 @@ COLVARS_SRCS = \
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colvarcomp_gpath.cpp \
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colvarcomp_gpath.cpp \
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colvarcomp_protein.cpp \
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colvarcomp_protein.cpp \
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colvarcomp_rotations.cpp \
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colvarcomp_rotations.cpp \
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colvarcomp_volmaps.cpp \
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colvar.cpp \
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colvar.cpp \
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colvardeps.cpp \
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colvardeps.cpp \
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colvargrid.cpp \
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colvargrid.cpp \
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@ -46,7 +47,12 @@ COLVARS_SRCS = \
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colvarparse.cpp \
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colvarparse.cpp \
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colvarproxy.cpp \
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colvarproxy.cpp \
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colvarproxy_replicas.cpp \
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colvarproxy_replicas.cpp \
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colvarproxy_tcl.cpp \
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colvarproxy_volmaps.cpp \
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colvarscript.cpp \
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colvarscript.cpp \
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colvarscript_commands.cpp \
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colvarscript_commands_bias.cpp \
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colvarscript_commands_colvar.cpp \
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colvartypes.cpp \
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colvartypes.cpp \
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colvarvalue.cpp
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colvarvalue.cpp
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@ -61,7 +67,7 @@ ifeq ($(COLVARS_LEPTON),no)
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LEPTON_INCFLAGS =
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LEPTON_INCFLAGS =
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COLVARS_OBJS = $(COLVARS_SRCS:.cpp=.o)
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COLVARS_OBJS = $(COLVARS_SRCS:.cpp=.o)
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else
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else
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LEPTON_INCFLAGS = -Ilepton/include -DLEPTON -DLEPTON_USE_STATIC_LIBRARIES
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LEPTON_INCFLAGS = -Ilepton/include -DLEPTON
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COLVARS_OBJS = $(COLVARS_SRCS:.cpp=.o) $(LEPTON_SRCS:.cpp=.o)
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COLVARS_OBJS = $(COLVARS_SRCS:.cpp=.o) $(LEPTON_SRCS:.cpp=.o)
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endif
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endif
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@ -77,25 +83,9 @@ Makefile.deps: $(COLVARS_SRCS)
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@echo > $@
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@echo > $@
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@for src in $^ ; do \
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@for src in $^ ; do \
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obj=`basename $$src .cpp`.o ; \
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obj=`basename $$src .cpp`.o ; \
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$(CXX) -MM $(COLVARS_INCFLAGS) $(LEPTON_INCFLAGS) \
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$(CXX) $(CXXFLAGS) -MM $(COLVARS_INCFLAGS) $(LEPTON_INCFLAGS) \
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-MT '$$(COLVARS_OBJ_DIR)'$$obj $$src >> $@ ; \
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-MT '$$(COLVARS_OBJ_DIR)'$$obj $$src >> $@ ; \
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done
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done
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include Makefile.deps
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include Makefile.deps
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# Exceptions to pattern rule above for Lepton objects
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lepton/src/CompiledExpression.o: lepton/src/CompiledExpression.cpp
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$(CXX) $(CXXFLAGS) -Ilepton/include -DLEPTON_BUILDING_STATIC_LIBRARY -c -o $@ $<
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lepton/src/ExpressionProgram.o: lepton/src/ExpressionProgram.cpp
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$(CXX) $(CXXFLAGS) -Ilepton/include -DLEPTON_BUILDING_STATIC_LIBRARY -c -o $@ $<
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lepton/src/ExpressionTreeNode.o: lepton/src/ExpressionTreeNode.cpp
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$(CXX) $(CXXFLAGS) -Ilepton/include -DLEPTON_BUILDING_STATIC_LIBRARY -c -o $@ $<
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lepton/src/Operation.o: lepton/src/Operation.cpp
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$(CXX) $(CXXFLAGS) -Ilepton/include -DLEPTON_BUILDING_STATIC_LIBRARY -c -o $@ $<
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lepton/src/ParsedExpression.o: lepton/src/ParsedExpression.cpp
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$(CXX) $(CXXFLAGS) -Ilepton/include -DLEPTON_BUILDING_STATIC_LIBRARY -c -o $@ $<
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lepton/src/Parser.o: lepton/src/Parser.cpp
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$(CXX) $(CXXFLAGS) -Ilepton/include -DLEPTON_BUILDING_STATIC_LIBRARY -c -o $@ $<
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include Makefile.lepton.deps # Hand-generated
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include Makefile.lepton.deps # Hand-generated
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@ -1,84 +1,103 @@
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$(COLVARS_OBJ_DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h \
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$(COLVARS_OBJ_DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h \
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colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
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colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
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colvarparse.h colvarparams.h colvaratoms.h colvardeps.h
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colvarproxy_tcl.h colvarproxy_volmaps.h colvarparse.h colvarparams.h \
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colvaratoms.h colvardeps.h
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$(COLVARS_OBJ_DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h \
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$(COLVARS_OBJ_DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h \
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colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvar.h \
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colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
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colvarparse.h colvarparams.h colvardeps.h colvarbias_abf.h colvarbias.h \
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colvarproxy_tcl.h colvarproxy_volmaps.h colvar.h colvarparse.h \
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colvargrid.h colvar_UIestimator.h
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colvarparams.h colvardeps.h colvarbias_abf.h colvarbias.h colvargrid.h \
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colvar_UIestimator.h
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$(COLVARS_OBJ_DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h \
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$(COLVARS_OBJ_DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h \
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colvars_version.h colvarbias.h colvar.h colvarvalue.h colvartypes.h \
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colvars_version.h colvarbias.h colvar.h colvarvalue.h colvartypes.h \
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colvarparse.h colvarparams.h colvardeps.h colvarbias_alb.h
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colvarparse.h colvarparams.h colvardeps.h colvarbias_alb.h
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$(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \
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$(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \
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colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvarbias.h \
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colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
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colvar.h colvarparse.h colvarparams.h colvardeps.h colvargrid.h
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colvarproxy_tcl.h colvarproxy_volmaps.h colvarbias.h colvar.h \
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colvarparse.h colvarparams.h colvardeps.h colvargrid.h
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$(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \
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$(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \
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colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
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colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
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colvarvalue.h colvar.h colvarparse.h colvarparams.h colvardeps.h \
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colvarvalue.h colvarproxy_tcl.h colvarproxy_volmaps.h colvar.h \
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colvarbias_histogram.h colvarbias.h colvargrid.h
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colvarparse.h colvarparams.h colvardeps.h colvarbias_histogram.h \
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colvarbias.h colvargrid.h
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$(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvarmodule.h \
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$(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvarmodule.h \
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colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvar.h \
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colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
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colvarparse.h colvarparams.h colvardeps.h colvarbias_meta.h colvarbias.h \
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colvarproxy_tcl.h colvarproxy_volmaps.h colvar.h colvarparse.h \
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colvargrid.h
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colvarparams.h colvardeps.h colvarbias_meta.h colvarbias.h colvargrid.h
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$(COLVARS_OBJ_DIR)colvarbias_restraint.o: colvarbias_restraint.cpp \
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$(COLVARS_OBJ_DIR)colvarbias_restraint.o: colvarbias_restraint.cpp \
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colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
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colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
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colvarvalue.h colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \
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colvarvalue.h colvarproxy_tcl.h colvarproxy_volmaps.h \
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colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \
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colvarparams.h colvardeps.h
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colvarparams.h colvardeps.h
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$(COLVARS_OBJ_DIR)colvarcomp_angles.o: colvarcomp_angles.cpp \
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$(COLVARS_OBJ_DIR)colvarcomp_angles.o: colvarcomp_angles.cpp \
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colvarmodule.h colvars_version.h colvar.h colvarvalue.h colvartypes.h \
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colvarmodule.h colvars_version.h colvar.h colvarvalue.h colvartypes.h \
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colvarparse.h colvarparams.h colvardeps.h colvarcomp.h colvaratoms.h \
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colvarparse.h colvarparams.h colvardeps.h colvarcomp.h colvaratoms.h \
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colvarproxy.h colvar_arithmeticpath.h colvar_geometricpath.h
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colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
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colvar_arithmeticpath.h colvar_geometricpath.h
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$(COLVARS_OBJ_DIR)colvarcomp_apath.o: colvarcomp_apath.cpp colvarmodule.h \
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$(COLVARS_OBJ_DIR)colvarcomp_apath.o: colvarcomp_apath.cpp colvarmodule.h \
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colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
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colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
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colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
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colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
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colvarproxy.h colvar_arithmeticpath.h colvar_geometricpath.h
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colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
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colvar_arithmeticpath.h colvar_geometricpath.h
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$(COLVARS_OBJ_DIR)colvarcomp_coordnums.o: colvarcomp_coordnums.cpp \
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$(COLVARS_OBJ_DIR)colvarcomp_coordnums.o: colvarcomp_coordnums.cpp \
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colvarmodule.h colvars_version.h colvarparse.h colvarvalue.h \
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colvarmodule.h colvars_version.h colvarparse.h colvarvalue.h \
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colvartypes.h colvarparams.h colvaratoms.h colvarproxy.h colvardeps.h \
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colvartypes.h colvarparams.h colvaratoms.h colvarproxy.h \
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colvar.h colvarcomp.h colvar_arithmeticpath.h colvar_geometricpath.h
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colvarproxy_tcl.h colvarproxy_volmaps.h colvardeps.h colvar.h \
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colvarcomp.h colvar_arithmeticpath.h colvar_geometricpath.h
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$(COLVARS_OBJ_DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h \
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$(COLVARS_OBJ_DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h \
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colvars_version.h colvarvalue.h colvartypes.h colvar.h colvarparse.h \
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colvars_version.h colvarvalue.h colvartypes.h colvar.h colvarparse.h \
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colvarparams.h colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h \
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colvarparams.h colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h \
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colvar_arithmeticpath.h colvar_geometricpath.h
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colvarproxy_tcl.h colvarproxy_volmaps.h colvar_arithmeticpath.h \
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colvar_geometricpath.h
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$(COLVARS_OBJ_DIR)colvarcomp_distances.o: colvarcomp_distances.cpp \
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$(COLVARS_OBJ_DIR)colvarcomp_distances.o: colvarcomp_distances.cpp \
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colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
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colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
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colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
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colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
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colvaratoms.h colvarproxy.h colvar_arithmeticpath.h \
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colvaratoms.h colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
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colvar_geometricpath.h
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colvar_arithmeticpath.h colvar_geometricpath.h
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$(COLVARS_OBJ_DIR)colvarcomp_gpath.o: colvarcomp_gpath.cpp colvarmodule.h \
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$(COLVARS_OBJ_DIR)colvarcomp_gpath.o: colvarcomp_gpath.cpp colvarmodule.h \
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colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
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colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
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colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
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colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
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colvarproxy.h colvar_arithmeticpath.h colvar_geometricpath.h
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colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
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colvar_arithmeticpath.h colvar_geometricpath.h
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$(COLVARS_OBJ_DIR)colvarcomp_protein.o: colvarcomp_protein.cpp \
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$(COLVARS_OBJ_DIR)colvarcomp_protein.o: colvarcomp_protein.cpp \
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colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
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colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
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colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
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colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
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||||||
colvaratoms.h colvarproxy.h colvar_arithmeticpath.h \
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colvaratoms.h colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
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||||||
colvar_geometricpath.h
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colvar_arithmeticpath.h colvar_geometricpath.h
|
||||||
$(COLVARS_OBJ_DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp \
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$(COLVARS_OBJ_DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp \
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||||||
colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
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colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
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||||||
colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
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colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
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||||||
colvaratoms.h colvarproxy.h colvar_arithmeticpath.h \
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colvaratoms.h colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
|
||||||
colvar_geometricpath.h
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colvar_arithmeticpath.h colvar_geometricpath.h
|
||||||
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$(COLVARS_OBJ_DIR)colvarcomp_volmaps.o: colvarcomp_volmaps.cpp \
|
||||||
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colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
|
||||||
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colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
|
||||||
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colvaratoms.h colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
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||||||
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colvar_arithmeticpath.h colvar_geometricpath.h
|
||||||
$(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \
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$(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \
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||||||
colvarvalue.h colvartypes.h colvarparse.h colvarparams.h colvar.h \
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colvarvalue.h colvartypes.h colvarparse.h colvarparams.h colvar.h \
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||||||
colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h \
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colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h colvarproxy_tcl.h \
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||||||
colvar_arithmeticpath.h colvar_geometricpath.h colvarscript.h \
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colvarproxy_volmaps.h colvar_arithmeticpath.h colvar_geometricpath.h \
|
||||||
colvarbias.h
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colvarscript.h colvarbias.h colvarscript_commands.h \
|
||||||
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colvarscript_commands_colvar.h colvarscript_commands_bias.h
|
||||||
$(COLVARS_OBJ_DIR)colvardeps.o: colvardeps.cpp colvarmodule.h \
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$(COLVARS_OBJ_DIR)colvardeps.o: colvardeps.cpp colvarmodule.h \
|
||||||
colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvardeps.h \
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colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
|
||||||
colvarparse.h colvarparams.h
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colvarproxy_tcl.h colvarproxy_volmaps.h colvardeps.h colvarparse.h \
|
||||||
|
colvarparams.h
|
||||||
$(COLVARS_OBJ_DIR)colvargrid.o: colvargrid.cpp colvarmodule.h \
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$(COLVARS_OBJ_DIR)colvargrid.o: colvargrid.cpp colvarmodule.h \
|
||||||
colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
|
colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
|
||||||
colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
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colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
|
||||||
colvarproxy.h colvar_arithmeticpath.h colvar_geometricpath.h \
|
colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
|
||||||
colvargrid.h
|
colvar_arithmeticpath.h colvar_geometricpath.h colvargrid.h
|
||||||
$(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \
|
$(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \
|
||||||
colvars_version.h colvarparse.h colvarvalue.h colvartypes.h \
|
colvars_version.h colvarparse.h colvarvalue.h colvartypes.h \
|
||||||
colvarparams.h colvarproxy.h colvar.h colvardeps.h colvarbias.h \
|
colvarparams.h colvarproxy.h colvarproxy_tcl.h colvarproxy_volmaps.h \
|
||||||
colvarbias_abf.h colvargrid.h colvar_UIestimator.h colvarbias_alb.h \
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colvar.h colvardeps.h colvarbias.h colvarbias_abf.h colvargrid.h \
|
||||||
colvarbias_histogram.h colvarbias_meta.h colvarbias_restraint.h \
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colvar_UIestimator.h colvarbias_alb.h colvarbias_histogram.h \
|
||||||
colvarscript.h colvaratoms.h colvarcomp.h colvar_arithmeticpath.h \
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colvarbias_meta.h colvarbias_restraint.h colvarscript.h \
|
||||||
colvar_geometricpath.h
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colvarscript_commands.h colvarscript_commands_colvar.h \
|
||||||
|
colvarscript_commands_bias.h colvaratoms.h colvarcomp.h \
|
||||||
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colvar_arithmeticpath.h colvar_geometricpath.h
|
||||||
$(COLVARS_OBJ_DIR)colvarparams.o: colvarparams.cpp colvarmodule.h \
|
$(COLVARS_OBJ_DIR)colvarparams.o: colvarparams.cpp colvarmodule.h \
|
||||||
colvars_version.h colvarvalue.h colvartypes.h colvarparams.h
|
colvars_version.h colvarvalue.h colvartypes.h colvarparams.h
|
||||||
$(COLVARS_OBJ_DIR)colvarparse.o: colvarparse.cpp colvarmodule.h \
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$(COLVARS_OBJ_DIR)colvarparse.o: colvarparse.cpp colvarmodule.h \
|
||||||
@ -86,15 +105,43 @@ $(COLVARS_OBJ_DIR)colvarparse.o: colvarparse.cpp colvarmodule.h \
|
|||||||
colvarparams.h
|
colvarparams.h
|
||||||
$(COLVARS_OBJ_DIR)colvarproxy.o: colvarproxy.cpp colvarmodule.h \
|
$(COLVARS_OBJ_DIR)colvarproxy.o: colvarproxy.cpp colvarmodule.h \
|
||||||
colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
|
colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
|
||||||
colvarscript.h colvarbias.h colvar.h colvarparse.h colvarparams.h \
|
colvarproxy_tcl.h colvarproxy_volmaps.h colvarscript.h colvarbias.h \
|
||||||
colvardeps.h colvaratoms.h
|
colvar.h colvarparse.h colvarparams.h colvardeps.h \
|
||||||
|
colvarscript_commands.h colvarscript_commands_colvar.h \
|
||||||
|
colvarscript_commands_bias.h colvaratoms.h
|
||||||
$(COLVARS_OBJ_DIR)colvarproxy_replicas.o: colvarproxy_replicas.cpp \
|
$(COLVARS_OBJ_DIR)colvarproxy_replicas.o: colvarproxy_replicas.cpp \
|
||||||
colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
|
colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
|
||||||
colvarvalue.h
|
colvarvalue.h colvarproxy_tcl.h colvarproxy_volmaps.h
|
||||||
$(COLVARS_OBJ_DIR)colvarscript.o: colvarscript.cpp colvarscript.h \
|
$(COLVARS_OBJ_DIR)colvarproxy_tcl.o: colvarproxy_tcl.cpp colvarmodule.h \
|
||||||
colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
|
colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
|
||||||
colvarbias.h colvar.h colvarparse.h colvarparams.h colvardeps.h \
|
colvarproxy_tcl.h colvarproxy_volmaps.h colvaratoms.h colvarparse.h \
|
||||||
colvarproxy.h
|
colvarparams.h colvardeps.h
|
||||||
|
$(COLVARS_OBJ_DIR)colvarproxy_volmaps.o: colvarproxy_volmaps.cpp \
|
||||||
|
colvarmodule.h colvars_version.h colvarproxy_volmaps.h
|
||||||
|
$(COLVARS_OBJ_DIR)colvarscript.o: colvarscript.cpp colvarproxy.h \
|
||||||
|
colvarmodule.h colvars_version.h colvartypes.h colvarvalue.h \
|
||||||
|
colvarproxy_tcl.h colvarproxy_volmaps.h colvardeps.h colvarparse.h \
|
||||||
|
colvarparams.h colvarscript.h colvarbias.h colvar.h \
|
||||||
|
colvarscript_commands.h colvarscript_commands_colvar.h \
|
||||||
|
colvarscript_commands_bias.h
|
||||||
|
$(COLVARS_OBJ_DIR)colvarscript_commands.o: colvarscript_commands.cpp \
|
||||||
|
colvarproxy.h colvarmodule.h colvars_version.h colvartypes.h \
|
||||||
|
colvarvalue.h colvarproxy_tcl.h colvarproxy_volmaps.h colvardeps.h \
|
||||||
|
colvarparse.h colvarparams.h colvarscript.h colvarbias.h colvar.h \
|
||||||
|
colvarscript_commands.h colvarscript_commands_colvar.h \
|
||||||
|
colvarscript_commands_bias.h
|
||||||
|
$(COLVARS_OBJ_DIR)colvarscript_commands_bias.o: \
|
||||||
|
colvarscript_commands_bias.cpp colvarproxy.h colvarmodule.h \
|
||||||
|
colvars_version.h colvartypes.h colvarvalue.h colvarproxy_tcl.h \
|
||||||
|
colvarproxy_volmaps.h colvardeps.h colvarparse.h colvarparams.h \
|
||||||
|
colvarscript.h colvarbias.h colvar.h colvarscript_commands.h \
|
||||||
|
colvarscript_commands_colvar.h colvarscript_commands_bias.h
|
||||||
|
$(COLVARS_OBJ_DIR)colvarscript_commands_colvar.o: \
|
||||||
|
colvarscript_commands_colvar.cpp colvarproxy.h colvarmodule.h \
|
||||||
|
colvars_version.h colvartypes.h colvarvalue.h colvarproxy_tcl.h \
|
||||||
|
colvarproxy_volmaps.h colvardeps.h colvarparse.h colvarparams.h \
|
||||||
|
colvarscript.h colvarbias.h colvar.h colvarscript_commands.h \
|
||||||
|
colvarscript_commands_colvar.h colvarscript_commands_bias.h
|
||||||
$(COLVARS_OBJ_DIR)colvartypes.o: colvartypes.cpp colvarmodule.h \
|
$(COLVARS_OBJ_DIR)colvartypes.o: colvartypes.cpp colvarmodule.h \
|
||||||
colvars_version.h colvartypes.h colvarparse.h colvarvalue.h \
|
colvars_version.h colvartypes.h colvarparse.h colvarvalue.h \
|
||||||
colvarparams.h
|
colvarparams.h
|
||||||
|
|||||||
@ -541,7 +541,7 @@ int colvar::init_grid_parameters(std::string const &conf)
|
|||||||
cvm::log("Reading legacy options lowerWall and lowerWallConstant: "
|
cvm::log("Reading legacy options lowerWall and lowerWallConstant: "
|
||||||
"consider using a harmonicWalls restraint (caution: force constant would then be scaled by width^2).\n");
|
"consider using a harmonicWalls restraint (caution: force constant would then be scaled by width^2).\n");
|
||||||
if (!get_keyval(conf, "lowerWall", lower_wall)) {
|
if (!get_keyval(conf, "lowerWall", lower_wall)) {
|
||||||
error_code != cvm::error("Error: the value of lowerWall must be set "
|
error_code |= cvm::error("Error: the value of lowerWall must be set "
|
||||||
"explicitly.\n", INPUT_ERROR);
|
"explicitly.\n", INPUT_ERROR);
|
||||||
}
|
}
|
||||||
lw_conf = std::string("\n\
|
lw_conf = std::string("\n\
|
||||||
@ -554,7 +554,7 @@ int colvar::init_grid_parameters(std::string const &conf)
|
|||||||
cvm::log("Reading legacy options upperWall and upperWallConstant: "
|
cvm::log("Reading legacy options upperWall and upperWallConstant: "
|
||||||
"consider using a harmonicWalls restraint (caution: force constant would then be scaled by width^2).\n");
|
"consider using a harmonicWalls restraint (caution: force constant would then be scaled by width^2).\n");
|
||||||
if (!get_keyval(conf, "upperWall", upper_wall)) {
|
if (!get_keyval(conf, "upperWall", upper_wall)) {
|
||||||
error_code != cvm::error("Error: the value of upperWall must be set "
|
error_code |= cvm::error("Error: the value of upperWall must be set "
|
||||||
"explicitly.\n", INPUT_ERROR);
|
"explicitly.\n", INPUT_ERROR);
|
||||||
}
|
}
|
||||||
uw_conf = std::string("\n\
|
uw_conf = std::string("\n\
|
||||||
@ -616,7 +616,7 @@ harmonicWalls {\n\
|
|||||||
"are enabled).\n", INPUT_ERROR);
|
"are enabled).\n", INPUT_ERROR);
|
||||||
}
|
}
|
||||||
|
|
||||||
return COLVARS_OK;
|
return error_code;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
@ -681,6 +681,9 @@ int colvar::init_extended_Lagrangian(std::string const &conf)
|
|||||||
// Adjust Langevin sigma for slow time step if time_step_factor != 1
|
// Adjust Langevin sigma for slow time step if time_step_factor != 1
|
||||||
ext_sigma = cvm::sqrt(2.0 * cvm::boltzmann() * temp * ext_gamma * ext_mass / (cvm::dt() * cvm::real(time_step_factor)));
|
ext_sigma = cvm::sqrt(2.0 * cvm::boltzmann() * temp * ext_gamma * ext_mass / (cvm::dt() * cvm::real(time_step_factor)));
|
||||||
}
|
}
|
||||||
|
|
||||||
|
get_keyval_feature(this, conf, "reflectingLowerBoundary", f_cv_reflecting_lower_boundary, false);
|
||||||
|
get_keyval_feature(this, conf, "reflectingUpperBoundary", f_cv_reflecting_upper_boundary, false);
|
||||||
}
|
}
|
||||||
|
|
||||||
return COLVARS_OK;
|
return COLVARS_OK;
|
||||||
@ -863,6 +866,8 @@ int colvar::init_components(std::string const &conf)
|
|||||||
error_code |= init_components_type<aspathCV>(conf, "arithmetic path collective variables (s) for other CVs", "aspathCV");
|
error_code |= init_components_type<aspathCV>(conf, "arithmetic path collective variables (s) for other CVs", "aspathCV");
|
||||||
error_code |= init_components_type<azpathCV>(conf, "arithmetic path collective variables (s) for other CVs", "azpathCV");
|
error_code |= init_components_type<azpathCV>(conf, "arithmetic path collective variables (s) for other CVs", "azpathCV");
|
||||||
|
|
||||||
|
error_code |= init_components_type<map_total>(conf, "total value of atomic map", "mapTotal");
|
||||||
|
|
||||||
if (!cvcs.size() || (error_code != COLVARS_OK)) {
|
if (!cvcs.size() || (error_code != COLVARS_OK)) {
|
||||||
cvm::error("Error: no valid components were provided "
|
cvm::error("Error: no valid components were provided "
|
||||||
"for this collective variable.\n",
|
"for this collective variable.\n",
|
||||||
@ -1040,85 +1045,93 @@ int colvar::init_dependencies() {
|
|||||||
init_feature(f_cv_gradient, "gradient", f_type_dynamic);
|
init_feature(f_cv_gradient, "gradient", f_type_dynamic);
|
||||||
require_feature_children(f_cv_gradient, f_cvc_gradient);
|
require_feature_children(f_cv_gradient, f_cvc_gradient);
|
||||||
|
|
||||||
init_feature(f_cv_collect_gradient, "collect gradient", f_type_dynamic);
|
init_feature(f_cv_collect_gradient, "collect_gradient", f_type_dynamic);
|
||||||
require_feature_self(f_cv_collect_gradient, f_cv_gradient);
|
require_feature_self(f_cv_collect_gradient, f_cv_gradient);
|
||||||
require_feature_self(f_cv_collect_gradient, f_cv_scalar);
|
require_feature_self(f_cv_collect_gradient, f_cv_scalar);
|
||||||
// The following exlusion could be lifted by implementing the feature
|
// The following exlusion could be lifted by implementing the feature
|
||||||
exclude_feature_self(f_cv_collect_gradient, f_cv_scripted);
|
exclude_feature_self(f_cv_collect_gradient, f_cv_scripted);
|
||||||
require_feature_children(f_cv_collect_gradient, f_cvc_explicit_gradient);
|
require_feature_children(f_cv_collect_gradient, f_cvc_explicit_gradient);
|
||||||
|
|
||||||
init_feature(f_cv_fdiff_velocity, "velocity from finite differences", f_type_dynamic);
|
init_feature(f_cv_fdiff_velocity, "velocity_from_finite_differences", f_type_dynamic);
|
||||||
|
|
||||||
// System force: either trivial (spring force); through extended Lagrangian, or calculated explicitly
|
// System force: either trivial (spring force); through extended Lagrangian, or calculated explicitly
|
||||||
init_feature(f_cv_total_force, "total force", f_type_dynamic);
|
init_feature(f_cv_total_force, "total_force", f_type_dynamic);
|
||||||
require_feature_alt(f_cv_total_force, f_cv_extended_Lagrangian, f_cv_total_force_calc);
|
require_feature_alt(f_cv_total_force, f_cv_extended_Lagrangian, f_cv_total_force_calc);
|
||||||
|
|
||||||
// Deps for explicit total force calculation
|
// Deps for explicit total force calculation
|
||||||
init_feature(f_cv_total_force_calc, "total force calculation", f_type_dynamic);
|
init_feature(f_cv_total_force_calc, "total_force_calculation", f_type_dynamic);
|
||||||
require_feature_self(f_cv_total_force_calc, f_cv_scalar);
|
require_feature_self(f_cv_total_force_calc, f_cv_scalar);
|
||||||
require_feature_self(f_cv_total_force_calc, f_cv_linear);
|
require_feature_self(f_cv_total_force_calc, f_cv_linear);
|
||||||
require_feature_children(f_cv_total_force_calc, f_cvc_inv_gradient);
|
require_feature_children(f_cv_total_force_calc, f_cvc_inv_gradient);
|
||||||
require_feature_self(f_cv_total_force_calc, f_cv_Jacobian);
|
require_feature_self(f_cv_total_force_calc, f_cv_Jacobian);
|
||||||
|
|
||||||
init_feature(f_cv_Jacobian, "Jacobian derivative", f_type_dynamic);
|
init_feature(f_cv_Jacobian, "Jacobian_derivative", f_type_dynamic);
|
||||||
require_feature_self(f_cv_Jacobian, f_cv_scalar);
|
require_feature_self(f_cv_Jacobian, f_cv_scalar);
|
||||||
require_feature_self(f_cv_Jacobian, f_cv_linear);
|
require_feature_self(f_cv_Jacobian, f_cv_linear);
|
||||||
require_feature_children(f_cv_Jacobian, f_cvc_Jacobian);
|
require_feature_children(f_cv_Jacobian, f_cvc_Jacobian);
|
||||||
|
|
||||||
init_feature(f_cv_hide_Jacobian, "hide Jacobian force", f_type_user);
|
init_feature(f_cv_hide_Jacobian, "hide_Jacobian_force", f_type_user);
|
||||||
require_feature_self(f_cv_hide_Jacobian, f_cv_Jacobian); // can only hide if calculated
|
require_feature_self(f_cv_hide_Jacobian, f_cv_Jacobian); // can only hide if calculated
|
||||||
|
|
||||||
init_feature(f_cv_extended_Lagrangian, "extended Lagrangian", f_type_user);
|
init_feature(f_cv_extended_Lagrangian, "extended_Lagrangian", f_type_user);
|
||||||
require_feature_self(f_cv_extended_Lagrangian, f_cv_scalar);
|
require_feature_self(f_cv_extended_Lagrangian, f_cv_scalar);
|
||||||
require_feature_self(f_cv_extended_Lagrangian, f_cv_gradient);
|
require_feature_self(f_cv_extended_Lagrangian, f_cv_gradient);
|
||||||
|
|
||||||
init_feature(f_cv_Langevin, "Langevin dynamics", f_type_user);
|
init_feature(f_cv_Langevin, "Langevin_dynamics", f_type_user);
|
||||||
require_feature_self(f_cv_Langevin, f_cv_extended_Lagrangian);
|
require_feature_self(f_cv_Langevin, f_cv_extended_Lagrangian);
|
||||||
|
|
||||||
init_feature(f_cv_single_cvc, "single component", f_type_static);
|
init_feature(f_cv_single_cvc, "single_component", f_type_static);
|
||||||
|
|
||||||
init_feature(f_cv_linear, "linear", f_type_static);
|
init_feature(f_cv_linear, "linear", f_type_static);
|
||||||
|
|
||||||
init_feature(f_cv_scalar, "scalar", f_type_static);
|
init_feature(f_cv_scalar, "scalar", f_type_static);
|
||||||
|
|
||||||
init_feature(f_cv_output_energy, "output energy", f_type_user);
|
init_feature(f_cv_output_energy, "output_energy", f_type_user);
|
||||||
|
|
||||||
init_feature(f_cv_output_value, "output value", f_type_user);
|
init_feature(f_cv_output_value, "output_value", f_type_user);
|
||||||
|
|
||||||
init_feature(f_cv_output_velocity, "output velocity", f_type_user);
|
init_feature(f_cv_output_velocity, "output_velocity", f_type_user);
|
||||||
require_feature_self(f_cv_output_velocity, f_cv_fdiff_velocity);
|
require_feature_self(f_cv_output_velocity, f_cv_fdiff_velocity);
|
||||||
|
|
||||||
init_feature(f_cv_output_applied_force, "output applied force", f_type_user);
|
init_feature(f_cv_output_applied_force, "output_applied_force", f_type_user);
|
||||||
|
|
||||||
init_feature(f_cv_output_total_force, "output total force", f_type_user);
|
init_feature(f_cv_output_total_force, "output_total_force", f_type_user);
|
||||||
require_feature_self(f_cv_output_total_force, f_cv_total_force);
|
require_feature_self(f_cv_output_total_force, f_cv_total_force);
|
||||||
|
|
||||||
init_feature(f_cv_subtract_applied_force, "subtract applied force from total force", f_type_user);
|
init_feature(f_cv_subtract_applied_force, "subtract_applied_force_from_total_force", f_type_user);
|
||||||
require_feature_self(f_cv_subtract_applied_force, f_cv_total_force);
|
require_feature_self(f_cv_subtract_applied_force, f_cv_total_force);
|
||||||
|
|
||||||
init_feature(f_cv_lower_boundary, "lower boundary", f_type_user);
|
init_feature(f_cv_lower_boundary, "lower_boundary", f_type_user);
|
||||||
require_feature_self(f_cv_lower_boundary, f_cv_scalar);
|
require_feature_self(f_cv_lower_boundary, f_cv_scalar);
|
||||||
|
|
||||||
init_feature(f_cv_upper_boundary, "upper boundary", f_type_user);
|
init_feature(f_cv_upper_boundary, "upper_boundary", f_type_user);
|
||||||
require_feature_self(f_cv_upper_boundary, f_cv_scalar);
|
require_feature_self(f_cv_upper_boundary, f_cv_scalar);
|
||||||
|
|
||||||
init_feature(f_cv_hard_lower_boundary, "hard lower boundary", f_type_user);
|
init_feature(f_cv_hard_lower_boundary, "hard_lower_boundary", f_type_user);
|
||||||
require_feature_self(f_cv_hard_lower_boundary, f_cv_lower_boundary);
|
require_feature_self(f_cv_hard_lower_boundary, f_cv_lower_boundary);
|
||||||
|
|
||||||
init_feature(f_cv_hard_upper_boundary, "hard upper boundary", f_type_user);
|
init_feature(f_cv_hard_upper_boundary, "hard_upper_boundary", f_type_user);
|
||||||
require_feature_self(f_cv_hard_upper_boundary, f_cv_upper_boundary);
|
require_feature_self(f_cv_hard_upper_boundary, f_cv_upper_boundary);
|
||||||
|
|
||||||
|
init_feature(f_cv_reflecting_lower_boundary, "reflecting_lower_boundary", f_type_user);
|
||||||
|
require_feature_self(f_cv_reflecting_lower_boundary, f_cv_lower_boundary);
|
||||||
|
require_feature_self(f_cv_reflecting_lower_boundary, f_cv_extended_Lagrangian);
|
||||||
|
|
||||||
|
init_feature(f_cv_reflecting_upper_boundary, "reflecting_upper_boundary", f_type_user);
|
||||||
|
require_feature_self(f_cv_reflecting_upper_boundary, f_cv_upper_boundary);
|
||||||
|
require_feature_self(f_cv_reflecting_upper_boundary, f_cv_extended_Lagrangian);
|
||||||
|
|
||||||
init_feature(f_cv_grid, "grid", f_type_dynamic);
|
init_feature(f_cv_grid, "grid", f_type_dynamic);
|
||||||
require_feature_self(f_cv_grid, f_cv_lower_boundary);
|
require_feature_self(f_cv_grid, f_cv_lower_boundary);
|
||||||
require_feature_self(f_cv_grid, f_cv_upper_boundary);
|
require_feature_self(f_cv_grid, f_cv_upper_boundary);
|
||||||
|
|
||||||
init_feature(f_cv_runave, "running average", f_type_user);
|
init_feature(f_cv_runave, "running_average", f_type_user);
|
||||||
|
|
||||||
init_feature(f_cv_corrfunc, "correlation function", f_type_user);
|
init_feature(f_cv_corrfunc, "correlation_function", f_type_user);
|
||||||
|
|
||||||
init_feature(f_cv_scripted, "scripted", f_type_user);
|
init_feature(f_cv_scripted, "scripted", f_type_user);
|
||||||
|
|
||||||
init_feature(f_cv_custom_function, "custom function", f_type_user);
|
init_feature(f_cv_custom_function, "custom_function", f_type_user);
|
||||||
exclude_feature_self(f_cv_custom_function, f_cv_scripted);
|
exclude_feature_self(f_cv_custom_function, f_cv_scripted);
|
||||||
|
|
||||||
init_feature(f_cv_periodic, "periodic", f_type_static);
|
init_feature(f_cv_periodic, "periodic", f_type_static);
|
||||||
@ -1129,7 +1142,7 @@ int colvar::init_dependencies() {
|
|||||||
|
|
||||||
// because total forces are obtained from the previous time step,
|
// because total forces are obtained from the previous time step,
|
||||||
// we cannot (currently) have colvar values and total forces for the same timestep
|
// we cannot (currently) have colvar values and total forces for the same timestep
|
||||||
init_feature(f_cv_multiple_ts, "multiple timestep colvar", f_type_static);
|
init_feature(f_cv_multiple_ts, "multiple_timestep", f_type_static);
|
||||||
exclude_feature_self(f_cv_multiple_ts, f_cv_total_force_calc);
|
exclude_feature_self(f_cv_multiple_ts, f_cv_total_force_calc);
|
||||||
|
|
||||||
// check that everything is initialized
|
// check that everything is initialized
|
||||||
@ -1199,8 +1212,17 @@ colvar::~colvar()
|
|||||||
(*ci)->remove_all_children();
|
(*ci)->remove_all_children();
|
||||||
delete *ci;
|
delete *ci;
|
||||||
}
|
}
|
||||||
|
cvcs.clear();
|
||||||
|
|
||||||
// remove reference to this colvar from the CVM
|
while (biases.size() > 0) {
|
||||||
|
size_t const i = biases.size()-1;
|
||||||
|
cvm::log("Warning: before deleting colvar " + name
|
||||||
|
+ ", deleting related bias " + biases[i]->name);
|
||||||
|
delete biases[i];
|
||||||
|
}
|
||||||
|
biases.clear();
|
||||||
|
|
||||||
|
// remove reference to this colvar from the module
|
||||||
colvarmodule *cv = cvm::main();
|
colvarmodule *cv = cvm::main();
|
||||||
for (std::vector<colvar *>::iterator cvi = cv->variables()->begin();
|
for (std::vector<colvar *>::iterator cvi = cv->variables()->begin();
|
||||||
cvi != cv->variables()->end();
|
cvi != cv->variables()->end();
|
||||||
@ -1211,6 +1233,8 @@ colvar::~colvar()
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
cv->config_changed();
|
||||||
|
|
||||||
#ifdef LEPTON
|
#ifdef LEPTON
|
||||||
for (std::vector<Lepton::CompiledExpression *>::iterator cei = value_evaluators.begin();
|
for (std::vector<Lepton::CompiledExpression *>::iterator cei = value_evaluators.begin();
|
||||||
cei != value_evaluators.end();
|
cei != value_evaluators.end();
|
||||||
@ -1599,6 +1623,15 @@ int colvar::calc_colvar_properties()
|
|||||||
// just calculated from the cvcs
|
// just calculated from the cvcs
|
||||||
if ((cvm::step_relative() == 0 && !after_restart) || x_ext.type() == colvarvalue::type_notset) {
|
if ((cvm::step_relative() == 0 && !after_restart) || x_ext.type() == colvarvalue::type_notset) {
|
||||||
x_ext = x;
|
x_ext = x;
|
||||||
|
if (is_enabled(f_cv_reflecting_lower_boundary) && x_ext < lower_boundary) {
|
||||||
|
cvm::log("Warning: initializing extended coordinate to reflective lower boundary, as colvar value is below.");
|
||||||
|
x_ext = lower_boundary;
|
||||||
|
}
|
||||||
|
if (is_enabled(f_cv_reflecting_upper_boundary) && x_ext > upper_boundary) {
|
||||||
|
cvm::log("Warning: initializing extended coordinate to reflective upper boundary, as colvar value is above.");
|
||||||
|
x_ext = upper_boundary;
|
||||||
|
}
|
||||||
|
|
||||||
v_ext.reset(); // (already 0; added for clarity)
|
v_ext.reset(); // (already 0; added for clarity)
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -1672,10 +1705,10 @@ cvm::real colvar::update_forces_energy()
|
|||||||
cvm::log("Updating extended-Lagrangian degree of freedom.\n");
|
cvm::log("Updating extended-Lagrangian degree of freedom.\n");
|
||||||
}
|
}
|
||||||
|
|
||||||
if (prev_timestep > -1) {
|
if (prev_timestep > -1L) {
|
||||||
// Keep track of slow timestep to integrate MTS colvars
|
// Keep track of slow timestep to integrate MTS colvars
|
||||||
// the colvar checks the interval after waking up twice
|
// the colvar checks the interval after waking up twice
|
||||||
int n_timesteps = cvm::step_relative() - prev_timestep;
|
cvm::step_number n_timesteps = cvm::step_relative() - prev_timestep;
|
||||||
if (n_timesteps != 0 && n_timesteps != time_step_factor) {
|
if (n_timesteps != 0 && n_timesteps != time_step_factor) {
|
||||||
cvm::error("Error: extended-Lagrangian " + description + " has timeStepFactor " +
|
cvm::error("Error: extended-Lagrangian " + description + " has timeStepFactor " +
|
||||||
cvm::to_str(time_step_factor) + ", but was activated after " + cvm::to_str(n_timesteps) +
|
cvm::to_str(time_step_factor) + ", but was activated after " + cvm::to_str(n_timesteps) +
|
||||||
@ -1737,6 +1770,14 @@ cvm::real colvar::update_forces_energy()
|
|||||||
}
|
}
|
||||||
v_ext += (0.5 * dt) * f_ext / ext_mass;
|
v_ext += (0.5 * dt) * f_ext / ext_mass;
|
||||||
x_ext += dt * v_ext;
|
x_ext += dt * v_ext;
|
||||||
|
|
||||||
|
cvm::real delta = 0; // Length of overshoot past either reflecting boundary
|
||||||
|
if ((is_enabled(f_cv_reflecting_lower_boundary) && (delta = x_ext - lower_boundary) < 0) ||
|
||||||
|
(is_enabled(f_cv_reflecting_upper_boundary) && (delta = x_ext - upper_boundary) > 0)) {
|
||||||
|
x_ext -= 2.0 * delta;
|
||||||
|
v_ext *= -1.0;
|
||||||
|
}
|
||||||
|
|
||||||
x_ext.apply_constraints();
|
x_ext.apply_constraints();
|
||||||
this->wrap(x_ext);
|
this->wrap(x_ext);
|
||||||
} else {
|
} else {
|
||||||
@ -2082,7 +2123,7 @@ void colvar::wrap(colvarvalue &x_unwrapped) const
|
|||||||
|
|
||||||
std::istream & colvar::read_state(std::istream &is)
|
std::istream & colvar::read_state(std::istream &is)
|
||||||
{
|
{
|
||||||
size_t const start_pos = is.tellg();
|
std::streampos const start_pos = is.tellg();
|
||||||
|
|
||||||
std::string conf;
|
std::string conf;
|
||||||
if ( !(is >> colvarparse::read_block("colvar", &conf)) ) {
|
if ( !(is >> colvarparse::read_block("colvar", &conf)) ) {
|
||||||
@ -2163,7 +2204,7 @@ std::istream & colvar::read_state(std::istream &is)
|
|||||||
|
|
||||||
std::istream & colvar::read_traj(std::istream &is)
|
std::istream & colvar::read_traj(std::istream &is)
|
||||||
{
|
{
|
||||||
size_t const start_pos = is.tellg();
|
std::streampos const start_pos = is.tellg();
|
||||||
|
|
||||||
if (is_enabled(f_cv_output_value)) {
|
if (is_enabled(f_cv_output_value)) {
|
||||||
|
|
||||||
|
|||||||
@ -602,6 +602,9 @@ public:
|
|||||||
class cartesian;
|
class cartesian;
|
||||||
class orientation;
|
class orientation;
|
||||||
|
|
||||||
|
// components that do not handle any atoms directly
|
||||||
|
class map_total;
|
||||||
|
|
||||||
protected:
|
protected:
|
||||||
|
|
||||||
/// \brief Array of \link colvar::cvc \endlink objects
|
/// \brief Array of \link colvar::cvc \endlink objects
|
||||||
|
|||||||
@ -116,7 +116,7 @@ namespace UIestimator {
|
|||||||
int i;
|
int i;
|
||||||
|
|
||||||
for (i = 0; i < dimension; i++) {
|
for (i = 0; i < dimension; i++) {
|
||||||
temp[i] = round((round(y[i] / width[i] + EPSILON) - round(x[i] / width[i] + EPSILON)) + (y_size - 1) / 2 + EPSILON);
|
temp[i] = int(round((round(y[i] / width[i] + EPSILON) - round(x[i] / width[i] + EPSILON)) + (y_size - 1) / 2 + EPSILON));
|
||||||
}
|
}
|
||||||
|
|
||||||
int index = 0;
|
int index = 0;
|
||||||
@ -305,12 +305,6 @@ namespace UIestimator {
|
|||||||
|
|
||||||
int i;
|
int i;
|
||||||
|
|
||||||
if (step % output_freq == 0) {
|
|
||||||
calc_pmf();
|
|
||||||
write_files();
|
|
||||||
//write_interal_data();
|
|
||||||
}
|
|
||||||
|
|
||||||
for (i = 0; i < dimension; i++) {
|
for (i = 0; i < dimension; i++) {
|
||||||
// for dihedral RC, it is possible that x = 179 and y = -179, should correct it
|
// for dihedral RC, it is possible that x = 179 and y = -179, should correct it
|
||||||
// may have problem, need to fix
|
// may have problem, need to fix
|
||||||
@ -381,6 +375,7 @@ namespace UIestimator {
|
|||||||
bool written;
|
bool written;
|
||||||
bool written_1D;
|
bool written_1D;
|
||||||
|
|
||||||
|
public:
|
||||||
// calculate gradients from the internal variables
|
// calculate gradients from the internal variables
|
||||||
void calc_pmf() {
|
void calc_pmf() {
|
||||||
int norm;
|
int norm;
|
||||||
|
|||||||
@ -240,19 +240,19 @@ int cvm::atom_group::init_dependencies() {
|
|||||||
}
|
}
|
||||||
|
|
||||||
init_feature(f_ag_active, "active", f_type_dynamic);
|
init_feature(f_ag_active, "active", f_type_dynamic);
|
||||||
init_feature(f_ag_center, "translational fit", f_type_static);
|
init_feature(f_ag_center, "translational_fit", f_type_static);
|
||||||
init_feature(f_ag_rotate, "rotational fit", f_type_static);
|
init_feature(f_ag_rotate, "rotational_fit", f_type_static);
|
||||||
init_feature(f_ag_fitting_group, "fitting group", f_type_static);
|
init_feature(f_ag_fitting_group, "fitting_group", f_type_static);
|
||||||
init_feature(f_ag_explicit_gradient, "explicit atom gradient", f_type_dynamic);
|
init_feature(f_ag_explicit_gradient, "explicit_atom_gradient", f_type_dynamic);
|
||||||
init_feature(f_ag_fit_gradients, "fit gradients", f_type_user);
|
init_feature(f_ag_fit_gradients, "fit_gradients", f_type_user);
|
||||||
require_feature_self(f_ag_fit_gradients, f_ag_explicit_gradient);
|
require_feature_self(f_ag_fit_gradients, f_ag_explicit_gradient);
|
||||||
|
|
||||||
init_feature(f_ag_atom_forces, "atomic forces", f_type_dynamic);
|
init_feature(f_ag_atom_forces, "atomic_forces", f_type_dynamic);
|
||||||
|
|
||||||
// parallel calculation implies that we have at least a scalable center of mass,
|
// parallel calculation implies that we have at least a scalable center of mass,
|
||||||
// but f_ag_scalable is kept as a separate feature to deal with future dependencies
|
// but f_ag_scalable is kept as a separate feature to deal with future dependencies
|
||||||
init_feature(f_ag_scalable, "scalable group calculation", f_type_static);
|
init_feature(f_ag_scalable, "scalable_group", f_type_static);
|
||||||
init_feature(f_ag_scalable_com, "scalable group center of mass calculation", f_type_static);
|
init_feature(f_ag_scalable_com, "scalable_group_center_of_mass", f_type_static);
|
||||||
require_feature_self(f_ag_scalable, f_ag_scalable_com);
|
require_feature_self(f_ag_scalable, f_ag_scalable_com);
|
||||||
|
|
||||||
// check that everything is initialized
|
// check that everything is initialized
|
||||||
|
|||||||
@ -7,6 +7,9 @@
|
|||||||
// If you wish to distribute your changes, please submit them to the
|
// If you wish to distribute your changes, please submit them to the
|
||||||
// Colvars repository at GitHub.
|
// Colvars repository at GitHub.
|
||||||
|
|
||||||
|
#include <fstream>
|
||||||
|
#include <cstring>
|
||||||
|
|
||||||
#include "colvarmodule.h"
|
#include "colvarmodule.h"
|
||||||
#include "colvarproxy.h"
|
#include "colvarproxy.h"
|
||||||
#include "colvarvalue.h"
|
#include "colvarvalue.h"
|
||||||
@ -23,8 +26,12 @@ colvarbias::colvarbias(char const *key)
|
|||||||
init_dependencies();
|
init_dependencies();
|
||||||
rank = 1;
|
rank = 1;
|
||||||
|
|
||||||
|
time_step_factor = 1;
|
||||||
|
|
||||||
has_data = false;
|
has_data = false;
|
||||||
b_output_energy = false;
|
b_output_energy = false;
|
||||||
|
output_freq = cvm::restart_out_freq;
|
||||||
|
|
||||||
reset();
|
reset();
|
||||||
state_file_step = 0L;
|
state_file_step = 0L;
|
||||||
matching_state = false;
|
matching_state = false;
|
||||||
@ -93,12 +100,18 @@ int colvarbias::init(std::string const &conf)
|
|||||||
|
|
||||||
output_prefix = cvm::output_prefix();
|
output_prefix = cvm::output_prefix();
|
||||||
|
|
||||||
|
get_keyval_feature(this, conf, "stepZeroData", f_cvb_step_zero_data, is_enabled(f_cvb_step_zero_data));
|
||||||
|
|
||||||
|
// Write energy to traj file?
|
||||||
get_keyval(conf, "outputEnergy", b_output_energy, b_output_energy);
|
get_keyval(conf, "outputEnergy", b_output_energy, b_output_energy);
|
||||||
|
|
||||||
// Disabled by default in base class; default value can be overridden by derived class constructor
|
// How often to write full output files?
|
||||||
get_keyval_feature(this, conf, "bypassExtendedLagrangian", f_cvb_bypass_ext_lagrangian, is_enabled(f_cvb_bypass_ext_lagrangian), parse_silent);
|
get_keyval(conf, "outputFreq", output_freq, output_freq);
|
||||||
|
|
||||||
get_keyval(conf, "timeStepFactor", time_step_factor, 1);
|
// Disabled by default in base class; default value can be overridden by derived class constructor
|
||||||
|
get_keyval_feature(this, conf, "bypassExtendedLagrangian", f_cvb_bypass_ext_lagrangian, is_enabled(f_cvb_bypass_ext_lagrangian), parse_echo);
|
||||||
|
|
||||||
|
get_keyval(conf, "timeStepFactor", time_step_factor, time_step_factor);
|
||||||
if (time_step_factor < 1) {
|
if (time_step_factor < 1) {
|
||||||
cvm::error("Error: timeStepFactor must be 1 or greater.\n");
|
cvm::error("Error: timeStepFactor must be 1 or greater.\n");
|
||||||
return COLVARS_ERROR;
|
return COLVARS_ERROR;
|
||||||
@ -125,37 +138,40 @@ int colvarbias::init_dependencies() {
|
|||||||
init_feature(f_cvb_awake, "awake", f_type_static);
|
init_feature(f_cvb_awake, "awake", f_type_static);
|
||||||
require_feature_self(f_cvb_awake, f_cvb_active);
|
require_feature_self(f_cvb_awake, f_cvb_active);
|
||||||
|
|
||||||
init_feature(f_cvb_apply_force, "apply force", f_type_user);
|
init_feature(f_cvb_step_zero_data, "step_zero_data", f_type_user);
|
||||||
|
|
||||||
|
init_feature(f_cvb_apply_force, "apply_force", f_type_user);
|
||||||
require_feature_children(f_cvb_apply_force, f_cv_gradient);
|
require_feature_children(f_cvb_apply_force, f_cv_gradient);
|
||||||
|
|
||||||
init_feature(f_cvb_bypass_ext_lagrangian, "bypass extended-Lagrangian coordinates", f_type_user);
|
init_feature(f_cvb_bypass_ext_lagrangian, "bypass_extended_Lagrangian_coordinates", f_type_user);
|
||||||
|
|
||||||
// The exclusion below prevents the inconsistency where biasing forces are applied onto
|
// The exclusion below prevents the inconsistency where biasing forces are applied onto
|
||||||
// the actual colvar, while total forces are measured on the extended coordinate
|
// the actual colvar, while total forces are measured on the extended coordinate
|
||||||
exclude_feature_self(f_cvb_bypass_ext_lagrangian, f_cvb_get_total_force);
|
exclude_feature_self(f_cvb_bypass_ext_lagrangian, f_cvb_get_total_force);
|
||||||
|
|
||||||
init_feature(f_cvb_get_total_force, "obtain total force", f_type_dynamic);
|
init_feature(f_cvb_get_total_force, "obtain_total_force", f_type_dynamic);
|
||||||
require_feature_children(f_cvb_get_total_force, f_cv_total_force);
|
require_feature_children(f_cvb_get_total_force, f_cv_total_force);
|
||||||
|
|
||||||
init_feature(f_cvb_output_acc_work, "output accumulated work", f_type_user);
|
init_feature(f_cvb_output_acc_work, "output_accumulated_work", f_type_user);
|
||||||
require_feature_self(f_cvb_output_acc_work, f_cvb_apply_force);
|
require_feature_self(f_cvb_output_acc_work, f_cvb_apply_force);
|
||||||
|
|
||||||
init_feature(f_cvb_history_dependent, "history-dependent", f_type_static);
|
init_feature(f_cvb_history_dependent, "history_dependent", f_type_static);
|
||||||
|
|
||||||
init_feature(f_cvb_time_dependent, "time-dependent", f_type_static);
|
init_feature(f_cvb_time_dependent, "time_dependent", f_type_static);
|
||||||
|
|
||||||
init_feature(f_cvb_scalar_variables, "require scalar variables", f_type_static);
|
init_feature(f_cvb_scalar_variables, "require_scalar_variables", f_type_static);
|
||||||
require_feature_children(f_cvb_scalar_variables, f_cv_scalar);
|
require_feature_children(f_cvb_scalar_variables, f_cv_scalar);
|
||||||
|
|
||||||
init_feature(f_cvb_calc_pmf, "calculate a PMF", f_type_static);
|
init_feature(f_cvb_calc_pmf, "calculate_a_PMF", f_type_static);
|
||||||
|
|
||||||
init_feature(f_cvb_calc_ti_samples, "calculate TI samples", f_type_dynamic);
|
init_feature(f_cvb_calc_ti_samples, "calculate_TI_samples", f_type_dynamic);
|
||||||
require_feature_self(f_cvb_calc_ti_samples, f_cvb_get_total_force);
|
require_feature_self(f_cvb_calc_ti_samples, f_cvb_get_total_force);
|
||||||
require_feature_children(f_cvb_calc_ti_samples, f_cv_grid);
|
require_feature_children(f_cvb_calc_ti_samples, f_cv_grid);
|
||||||
|
|
||||||
init_feature(f_cvb_write_ti_samples, "write TI samples ", f_type_user);
|
init_feature(f_cvb_write_ti_samples, "write_TI_samples_", f_type_user);
|
||||||
require_feature_self(f_cvb_write_ti_samples, f_cvb_calc_ti_samples);
|
require_feature_self(f_cvb_write_ti_samples, f_cvb_calc_ti_samples);
|
||||||
|
|
||||||
init_feature(f_cvb_write_ti_pmf, "write TI PMF", f_type_user);
|
init_feature(f_cvb_write_ti_pmf, "write_TI_PMF", f_type_user);
|
||||||
require_feature_self(f_cvb_write_ti_pmf, f_cvb_calc_ti_samples);
|
require_feature_self(f_cvb_write_ti_pmf, f_cvb_calc_ti_samples);
|
||||||
|
|
||||||
// check that everything is initialized
|
// check that everything is initialized
|
||||||
@ -237,6 +253,8 @@ int colvarbias::clear()
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
cv->config_changed();
|
||||||
|
|
||||||
return COLVARS_OK;
|
return COLVARS_OK;
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -302,6 +320,17 @@ int colvarbias::update()
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
bool colvarbias::can_accumulate_data()
|
||||||
|
{
|
||||||
|
colvarproxy *proxy = cvm::main()->proxy;
|
||||||
|
if (((cvm::step_relative() > 0) && !proxy->simulation_continuing()) ||
|
||||||
|
is_enabled(f_cvb_step_zero_data)) {
|
||||||
|
return true;
|
||||||
|
}
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
int colvarbias::calc_energy(std::vector<colvarvalue> const *)
|
int colvarbias::calc_energy(std::vector<colvarvalue> const *)
|
||||||
{
|
{
|
||||||
bias_energy = 0.0;
|
bias_energy = 0.0;
|
||||||
@ -451,7 +480,7 @@ std::ostream & colvarbias::write_state(std::ostream &os)
|
|||||||
|
|
||||||
std::istream & colvarbias::read_state(std::istream &is)
|
std::istream & colvarbias::read_state(std::istream &is)
|
||||||
{
|
{
|
||||||
size_t const start_pos = is.tellg();
|
std::streampos const start_pos = is.tellg();
|
||||||
|
|
||||||
std::string key, brace, conf;
|
std::string key, brace, conf;
|
||||||
if ( !(is >> key) || !(key == state_keyword || key == bias_type) ||
|
if ( !(is >> key) || !(key == state_keyword || key == bias_type) ||
|
||||||
@ -501,12 +530,80 @@ std::istream & colvarbias::read_state(std::istream &is)
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int colvarbias::write_state_prefix(std::string const &prefix)
|
||||||
|
{
|
||||||
|
std::string const filename =
|
||||||
|
cvm::state_file_prefix(prefix.c_str())+".colvars.state";
|
||||||
|
std::ostream *os = cvm::proxy->output_stream(filename.c_str());
|
||||||
|
int error_code = COLVARS_OK;
|
||||||
|
if (os != NULL) {
|
||||||
|
os->setf(std::ios::scientific, std::ios::floatfield);
|
||||||
|
error_code = write_state(*os).good() ? COLVARS_OK : FILE_ERROR;
|
||||||
|
} else {
|
||||||
|
error_code = FILE_ERROR;
|
||||||
|
}
|
||||||
|
cvm::proxy->close_output_stream(filename.c_str());
|
||||||
|
return error_code;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int colvarbias::write_state_string(std::string &output)
|
||||||
|
{
|
||||||
|
std::ostringstream os;
|
||||||
|
if (!write_state(os)) {
|
||||||
|
return cvm::error("Error: in writing state of bias \""+name+
|
||||||
|
"\" to buffer.\n", FILE_ERROR);
|
||||||
|
}
|
||||||
|
output = os.str();
|
||||||
|
return COLVARS_OK;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int colvarbias::read_state_prefix(std::string const &prefix)
|
||||||
|
{
|
||||||
|
std::string filename((prefix+std::string(".colvars.state")).c_str());
|
||||||
|
std::ifstream is(filename.c_str());
|
||||||
|
if (!is.good()) {
|
||||||
|
// try without the suffix
|
||||||
|
is.clear();
|
||||||
|
filename = prefix;
|
||||||
|
is.open(filename.c_str());
|
||||||
|
}
|
||||||
|
return read_state(is).good() ? COLVARS_OK :
|
||||||
|
cvm::error("Error: in reading state for \""+name+"\" from input file \""+
|
||||||
|
std::string(filename)+"\".\n", FILE_ERROR);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int colvarbias::read_state_string(char const *buffer)
|
||||||
|
{
|
||||||
|
if (buffer != NULL) {
|
||||||
|
size_t const buffer_size = strlen(buffer);
|
||||||
|
if (cvm::debug()) {
|
||||||
|
cvm::log("colvarbias::read_state_string() with argument:\n");
|
||||||
|
cvm::log(buffer);
|
||||||
|
}
|
||||||
|
|
||||||
|
if (buffer_size > 0) {
|
||||||
|
std::istringstream is;
|
||||||
|
is.rdbuf()->pubsetbuf(const_cast<char *>(buffer), buffer_size);
|
||||||
|
return read_state(is).good() ? COLVARS_OK :
|
||||||
|
cvm::error("Error: in reading state for \""+name+"\" from buffer.\n",
|
||||||
|
FILE_ERROR);
|
||||||
|
}
|
||||||
|
return COLVARS_OK;
|
||||||
|
}
|
||||||
|
return cvm::error("Error: NULL pointer for colvarbias::read_state_string()",
|
||||||
|
BUG_ERROR);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
std::istream & colvarbias::read_state_data_key(std::istream &is, char const *key)
|
std::istream & colvarbias::read_state_data_key(std::istream &is, char const *key)
|
||||||
{
|
{
|
||||||
size_t const start_pos = is.tellg();
|
std::streampos const start_pos = is.tellg();
|
||||||
std::string key_in;
|
std::string key_in;
|
||||||
if ( !(is >> key_in) ||
|
if ( !(is >> key_in) ||
|
||||||
!(key_in == to_lower_cppstr(std::string(key))) ) {
|
!(to_lower_cppstr(key_in) == to_lower_cppstr(std::string(key))) ) {
|
||||||
cvm::error("Error: in reading restart configuration for "+
|
cvm::error("Error: in reading restart configuration for "+
|
||||||
bias_type+" bias \""+this->name+"\" at position "+
|
bias_type+" bias \""+this->name+"\" at position "+
|
||||||
cvm::to_str(static_cast<size_t>(is.tellg()))+
|
cvm::to_str(static_cast<size_t>(is.tellg()))+
|
||||||
@ -546,7 +643,12 @@ std::ostream & colvarbias::write_traj(std::ostream &os)
|
|||||||
colvarbias_ti::colvarbias_ti(char const *key)
|
colvarbias_ti::colvarbias_ti(char const *key)
|
||||||
: colvarbias(key)
|
: colvarbias(key)
|
||||||
{
|
{
|
||||||
|
colvarproxy *proxy = cvm::main()->proxy;
|
||||||
provide(f_cvb_calc_ti_samples);
|
provide(f_cvb_calc_ti_samples);
|
||||||
|
if (!proxy->total_forces_same_step()) {
|
||||||
|
// Samples at step zero can not be collected
|
||||||
|
feature_states[f_cvb_step_zero_data].available = false;
|
||||||
|
}
|
||||||
ti_avg_forces = NULL;
|
ti_avg_forces = NULL;
|
||||||
ti_count = NULL;
|
ti_count = NULL;
|
||||||
}
|
}
|
||||||
@ -683,9 +785,11 @@ int colvarbias_ti::update_system_forces(std::vector<colvarvalue> const
|
|||||||
(*subtract_forces)[i] : previous_colvar_forces[i]);
|
(*subtract_forces)[i] : previous_colvar_forces[i]);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
if (cvm::step_relative() > 0 || is_enabled(f_cvb_step_zero_data)) {
|
||||||
ti_avg_forces->acc_value(ti_bin, ti_system_forces);
|
ti_avg_forces->acc_value(ti_bin, ti_system_forces);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
}
|
||||||
|
|
||||||
if (!proxy->total_forces_same_step()) {
|
if (!proxy->total_forces_same_step()) {
|
||||||
// Set the index for use in the next iteration, when total forces come in
|
// Set the index for use in the next iteration, when total forces come in
|
||||||
|
|||||||
@ -57,6 +57,10 @@ public:
|
|||||||
/// Some implementations may use calc_energy() and calc_forces()
|
/// Some implementations may use calc_energy() and calc_forces()
|
||||||
virtual int update();
|
virtual int update();
|
||||||
|
|
||||||
|
/// Returns true if the current step represent a valid increment, whose data
|
||||||
|
/// can be recorded (as opposed to e.g. a continuation step from a restart)
|
||||||
|
virtual bool can_accumulate_data();
|
||||||
|
|
||||||
/// Compute the energy of the bias
|
/// Compute the energy of the bias
|
||||||
/// Uses the vector of colvar values provided if not NULL, and the values
|
/// Uses the vector of colvar values provided if not NULL, and the values
|
||||||
/// currently cached in the bias instance otherwise
|
/// currently cached in the bias instance otherwise
|
||||||
@ -144,14 +148,28 @@ public:
|
|||||||
}
|
}
|
||||||
|
|
||||||
/// Read a keyword from the state data (typically a header)
|
/// Read a keyword from the state data (typically a header)
|
||||||
|
/// \param Input stream
|
||||||
|
/// \param Keyword labeling the header block
|
||||||
std::istream & read_state_data_key(std::istream &is, char const *key);
|
std::istream & read_state_data_key(std::istream &is, char const *key);
|
||||||
|
|
||||||
/// Write the bias configuration to a restart file or other stream
|
/// Write the bias configuration to a state file or other stream
|
||||||
std::ostream & write_state(std::ostream &os);
|
std::ostream & write_state(std::ostream &os);
|
||||||
|
|
||||||
/// Read the bias configuration from a restart file or other stream
|
/// Read the bias configuration from a restart file or other stream
|
||||||
std::istream & read_state(std::istream &is);
|
std::istream & read_state(std::istream &is);
|
||||||
|
|
||||||
|
/// Write the bias state to a file with the given prefix
|
||||||
|
int write_state_prefix(std::string const &prefix);
|
||||||
|
|
||||||
|
/// Write the bias state to a string
|
||||||
|
int write_state_string(std::string &output);
|
||||||
|
|
||||||
|
/// Read the bias state from a file with this name or prefix
|
||||||
|
int read_state_prefix(std::string const &prefix);
|
||||||
|
|
||||||
|
/// Read the bias state from this string buffer
|
||||||
|
int read_state_string(char const *buffer);
|
||||||
|
|
||||||
/// Write a label to the trajectory file (comment line)
|
/// Write a label to the trajectory file (comment line)
|
||||||
virtual std::ostream & write_traj_label(std::ostream &os);
|
virtual std::ostream & write_traj_label(std::ostream &os);
|
||||||
|
|
||||||
@ -164,6 +182,9 @@ public:
|
|||||||
return COLVARS_OK;
|
return COLVARS_OK;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/// Frequency for writing output files
|
||||||
|
size_t output_freq;
|
||||||
|
|
||||||
/// Write any output files that this bias may have (e.g. PMF files)
|
/// Write any output files that this bias may have (e.g. PMF files)
|
||||||
virtual int write_output_files()
|
virtual int write_output_files()
|
||||||
{
|
{
|
||||||
|
|||||||
@ -8,7 +8,6 @@
|
|||||||
// Colvars repository at GitHub.
|
// Colvars repository at GitHub.
|
||||||
|
|
||||||
#include "colvarmodule.h"
|
#include "colvarmodule.h"
|
||||||
#include "colvarproxy.h"
|
|
||||||
#include "colvar.h"
|
#include "colvar.h"
|
||||||
#include "colvarbias_abf.h"
|
#include "colvarbias_abf.h"
|
||||||
|
|
||||||
@ -29,8 +28,14 @@ colvarbias_abf::colvarbias_abf(char const *key)
|
|||||||
last_gradients(NULL),
|
last_gradients(NULL),
|
||||||
last_samples(NULL)
|
last_samples(NULL)
|
||||||
{
|
{
|
||||||
|
colvarproxy *proxy = cvm::main()->proxy;
|
||||||
|
if (!proxy->total_forces_same_step()) {
|
||||||
|
// Samples at step zero can not be collected
|
||||||
|
feature_states[f_cvb_step_zero_data].available = false;
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
int colvarbias_abf::init(std::string const &conf)
|
int colvarbias_abf::init(std::string const &conf)
|
||||||
{
|
{
|
||||||
colvarbias::init(conf);
|
colvarbias::init(conf);
|
||||||
@ -71,8 +76,19 @@ int colvarbias_abf::init(std::string const &conf)
|
|||||||
// full_samples - min_samples >= 1 is guaranteed
|
// full_samples - min_samples >= 1 is guaranteed
|
||||||
|
|
||||||
get_keyval(conf, "inputPrefix", input_prefix, std::vector<std::string>());
|
get_keyval(conf, "inputPrefix", input_prefix, std::vector<std::string>());
|
||||||
get_keyval(conf, "outputFreq", output_freq, cvm::restart_out_freq);
|
|
||||||
get_keyval(conf, "historyFreq", history_freq, 0);
|
get_keyval(conf, "historyFreq", history_freq, 0);
|
||||||
|
if (history_freq != 0) {
|
||||||
|
if (output_freq == 0) {
|
||||||
|
cvm::error("Error: historyFreq must be a multiple of outputFreq.\n",
|
||||||
|
INPUT_ERROR);
|
||||||
|
} else {
|
||||||
|
if ((history_freq % output_freq) != 0) {
|
||||||
|
cvm::error("Error: historyFreq must be a multiple of outputFreq.\n",
|
||||||
|
INPUT_ERROR);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
b_history_files = (history_freq > 0);
|
b_history_files = (history_freq > 0);
|
||||||
|
|
||||||
// shared ABF
|
// shared ABF
|
||||||
@ -146,6 +162,7 @@ int colvarbias_abf::init(std::string const &conf)
|
|||||||
for (i = 0; i < num_variables(); i++) {
|
for (i = 0; i < num_variables(); i++) {
|
||||||
if (max_force[i] < 0.0) {
|
if (max_force[i] < 0.0) {
|
||||||
cvm::error("Error: maxForce should be non-negative.");
|
cvm::error("Error: maxForce should be non-negative.");
|
||||||
|
return COLVARS_ERROR;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
cap_force = true;
|
cap_force = true;
|
||||||
@ -184,25 +201,24 @@ int colvarbias_abf::init(std::string const &conf)
|
|||||||
czar_gradients = new colvar_grid_gradient(colvars);
|
czar_gradients = new colvar_grid_gradient(colvars);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
get_keyval(conf, "integrate", b_integrate, num_variables() <= 3); // Integrate for output if d<=3
|
||||||
|
if (b_integrate) {
|
||||||
// For now, we integrate on-the-fly iff the grid is < 3D
|
// For now, we integrate on-the-fly iff the grid is < 3D
|
||||||
if ( num_variables() <= 3 ) {
|
if ( num_variables() > 3 ) {
|
||||||
|
cvm::error("Error: cannot integrate free energy in dimension > 3.\n");
|
||||||
|
return COLVARS_ERROR;
|
||||||
|
}
|
||||||
pmf = new integrate_potential(colvars, gradients);
|
pmf = new integrate_potential(colvars, gradients);
|
||||||
if ( b_CZAR_estimator ) {
|
if ( b_CZAR_estimator ) {
|
||||||
czar_pmf = new integrate_potential(colvars, czar_gradients);
|
czar_pmf = new integrate_potential(colvars, czar_gradients);
|
||||||
}
|
}
|
||||||
get_keyval(conf, "integrate", b_integrate, true); // Integrate for output
|
|
||||||
if ( num_variables() > 1 ) {
|
|
||||||
// Projected ABF
|
|
||||||
get_keyval(conf, "pABFintegrateFreq", pabf_freq, 0);
|
|
||||||
// Parameters for integrating initial (and final) gradient data
|
// Parameters for integrating initial (and final) gradient data
|
||||||
get_keyval(conf, "integrateInitMaxIterations", integrate_initial_iterations, 1e4);
|
get_keyval(conf, "integrateMaxIterations", integrate_iterations, 1e4, colvarparse::parse_silent);
|
||||||
get_keyval(conf, "integrateInitTol", integrate_initial_tol, 1e-6);
|
get_keyval(conf, "integrateTol", integrate_tol, 1e-6, colvarparse::parse_silent);
|
||||||
// for updating the integrated PMF on the fly
|
// Projected ABF, updating the integrated PMF on the fly
|
||||||
get_keyval(conf, "integrateMaxIterations", integrate_iterations, 100);
|
get_keyval(conf, "pABFintegrateFreq", pabf_freq, 0, colvarparse::parse_silent);
|
||||||
get_keyval(conf, "integrateTol", integrate_tol, 1e-4);
|
get_keyval(conf, "pABFintegrateMaxIterations", pabf_integrate_iterations, 100, colvarparse::parse_silent);
|
||||||
}
|
get_keyval(conf, "pABFintegrateTol", pabf_integrate_tol, 1e-4, colvarparse::parse_silent);
|
||||||
} else {
|
|
||||||
b_integrate = false;
|
|
||||||
}
|
}
|
||||||
|
|
||||||
// For shared ABF, we store a second set of grids.
|
// For shared ABF, we store a second set of grids.
|
||||||
@ -330,7 +346,7 @@ int colvarbias_abf::update()
|
|||||||
force_bin = bin;
|
force_bin = bin;
|
||||||
}
|
}
|
||||||
|
|
||||||
if (cvm::step_relative() > 0 || cvm::proxy->total_forces_same_step()) {
|
if (cvm::step_relative() > 0 || is_enabled(f_cvb_step_zero_data)) {
|
||||||
|
|
||||||
if (update_bias) {
|
if (update_bias) {
|
||||||
// if (b_adiabatic_reweighting) {
|
// if (b_adiabatic_reweighting) {
|
||||||
@ -370,10 +386,10 @@ int colvarbias_abf::update()
|
|||||||
if ( b_integrate ) {
|
if ( b_integrate ) {
|
||||||
if ( pabf_freq && cvm::step_relative() % pabf_freq == 0 ) {
|
if ( pabf_freq && cvm::step_relative() % pabf_freq == 0 ) {
|
||||||
cvm::real err;
|
cvm::real err;
|
||||||
int iter = pmf->integrate(integrate_iterations, integrate_tol, err);
|
int iter = pmf->integrate(pabf_integrate_iterations, pabf_integrate_tol, err);
|
||||||
if ( iter == integrate_iterations ) {
|
if ( iter == pabf_integrate_iterations ) {
|
||||||
cvm::log("Warning: PMF integration did not converge to " + cvm::to_str(integrate_tol)
|
cvm::log("Warning: PMF integration did not converge to " + cvm::to_str(pabf_integrate_tol)
|
||||||
+ " in " + cvm::to_str(integrate_iterations)
|
+ " in " + cvm::to_str(pabf_integrate_iterations)
|
||||||
+ " steps. Residual error: " + cvm::to_str(err));
|
+ " steps. Residual error: " + cvm::to_str(err));
|
||||||
}
|
}
|
||||||
pmf->set_zero_minimum(); // TODO: do this only when necessary
|
pmf->set_zero_minimum(); // TODO: do this only when necessary
|
||||||
@ -448,17 +464,6 @@ int colvarbias_abf::update()
|
|||||||
output_prefix = cvm::output_prefix() + "." + this->name;
|
output_prefix = cvm::output_prefix() + "." + this->name;
|
||||||
}
|
}
|
||||||
|
|
||||||
if (output_freq && (cvm::step_absolute() % output_freq) == 0) {
|
|
||||||
if (cvm::debug()) cvm::log("ABF bias trying to write gradients and samples to disk");
|
|
||||||
write_gradients_samples(output_prefix);
|
|
||||||
}
|
|
||||||
|
|
||||||
if (b_history_files && (cvm::step_absolute() % history_freq) == 0) {
|
|
||||||
// file already exists iff cvm::step_relative() > 0
|
|
||||||
// otherwise, backup and replace
|
|
||||||
write_gradients_samples(output_prefix + ".hist", (cvm::step_relative() > 0));
|
|
||||||
}
|
|
||||||
|
|
||||||
if (shared_on && shared_last_step >= 0 && cvm::step_absolute() % shared_freq == 0) {
|
if (shared_on && shared_last_step >= 0 && cvm::step_absolute() % shared_freq == 0) {
|
||||||
// Share gradients and samples for shared ABF.
|
// Share gradients and samples for shared ABF.
|
||||||
replica_share();
|
replica_share();
|
||||||
@ -487,10 +492,10 @@ int colvarbias_abf::update()
|
|||||||
eabf_UI.update(cvm::step_absolute(), x, y);
|
eabf_UI.update(cvm::step_absolute(), x, y);
|
||||||
}
|
}
|
||||||
|
|
||||||
/// Add the bias energy for 1D ABF
|
/// Compute the bias energy
|
||||||
bias_energy = calc_energy(NULL);
|
int error_code = calc_energy(NULL);
|
||||||
|
|
||||||
return COLVARS_OK;
|
return error_code;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
@ -570,83 +575,71 @@ int colvarbias_abf::replica_share() {
|
|||||||
last_samples->copy_grid(*samples);
|
last_samples->copy_grid(*samples);
|
||||||
shared_last_step = cvm::step_absolute();
|
shared_last_step = cvm::step_absolute();
|
||||||
|
|
||||||
|
if (b_integrate) {
|
||||||
|
// Update divergence to account for newly shared gradients
|
||||||
|
pmf->set_div();
|
||||||
|
}
|
||||||
return COLVARS_OK;
|
return COLVARS_OK;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
template <class T> int colvarbias_abf::write_grid_to_file(T const *grid,
|
||||||
void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool append)
|
std::string const &filename,
|
||||||
{
|
bool close) {
|
||||||
std::string samples_out_name = prefix + ".count";
|
std::ostream *os = cvm::proxy->output_stream(filename);
|
||||||
std::string gradients_out_name = prefix + ".grad";
|
if (!os) {
|
||||||
std::ios::openmode mode = (append ? std::ios::app : std::ios::out);
|
return cvm::error("Error opening file " + filename + " for writing.\n", COLVARS_ERROR | FILE_ERROR);
|
||||||
|
}
|
||||||
std::ostream *samples_os =
|
grid->write_multicol(*os);
|
||||||
cvm::proxy->output_stream(samples_out_name, mode);
|
if (close) {
|
||||||
if (!samples_os) return;
|
cvm::proxy->close_output_stream(filename);
|
||||||
samples->write_multicol(*samples_os);
|
} else {
|
||||||
cvm::proxy->close_output_stream(samples_out_name);
|
// Insert empty line between frames in history files
|
||||||
|
*os << std::endl;
|
||||||
// In dimension higher than 2, dx is easier to handle and visualize
|
cvm::proxy->flush_output_stream(os);
|
||||||
if (num_variables() > 2) {
|
|
||||||
std::string samples_dx_out_name = prefix + ".count.dx";
|
|
||||||
std::ostream *samples_dx_os = cvm::proxy->output_stream(samples_dx_out_name, mode);
|
|
||||||
if (!samples_os) return;
|
|
||||||
samples->write_opendx(*samples_dx_os);
|
|
||||||
*samples_dx_os << std::endl;
|
|
||||||
cvm::proxy->close_output_stream(samples_dx_out_name);
|
|
||||||
}
|
}
|
||||||
|
|
||||||
std::ostream *gradients_os =
|
// In dimension higher than 2, dx is easier to handle and visualize
|
||||||
cvm::proxy->output_stream(gradients_out_name, mode);
|
// but we cannot write multiple frames in a dx file now
|
||||||
if (!gradients_os) return;
|
// (could be implemented as multiple dx files)
|
||||||
gradients->write_multicol(*gradients_os);
|
if (num_variables() > 2 && close) {
|
||||||
cvm::proxy->close_output_stream(gradients_out_name);
|
std::string dx = filename + ".dx";
|
||||||
|
std::ostream *dx_os = cvm::proxy->output_stream(dx);
|
||||||
|
if (!dx_os) {
|
||||||
|
return cvm::error("Error opening file " + dx + " for writing.\n", COLVARS_ERROR | FILE_ERROR);
|
||||||
|
}
|
||||||
|
grid->write_opendx(*dx_os);
|
||||||
|
// if (close) {
|
||||||
|
cvm::proxy->close_output_stream(dx);
|
||||||
|
// }
|
||||||
|
// else {
|
||||||
|
// // TODO, decide convention for multiple datasets in dx file
|
||||||
|
// *dx_os << std::endl;
|
||||||
|
// dx_os->flush();
|
||||||
|
// }
|
||||||
|
}
|
||||||
|
return COLVARS_OK;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool close)
|
||||||
|
{
|
||||||
|
write_grid_to_file<colvar_grid_count>(samples, prefix + ".count", close);
|
||||||
|
write_grid_to_file<colvar_grid_gradient>(gradients, prefix + ".grad", close);
|
||||||
|
|
||||||
if (b_integrate) {
|
if (b_integrate) {
|
||||||
// Do numerical integration (to high precision) and output a PMF
|
// Do numerical integration (to high precision) and output a PMF
|
||||||
cvm::real err;
|
cvm::real err;
|
||||||
pmf->integrate(integrate_initial_iterations, integrate_initial_tol, err);
|
pmf->integrate(integrate_iterations, integrate_tol, err);
|
||||||
pmf->set_zero_minimum();
|
pmf->set_zero_minimum();
|
||||||
|
write_grid_to_file<colvar_grid_scalar>(pmf, prefix + ".pmf", close);
|
||||||
std::string pmf_out_name = prefix + ".pmf";
|
|
||||||
std::ostream *pmf_os = cvm::proxy->output_stream(pmf_out_name, mode);
|
|
||||||
if (!pmf_os) return;
|
|
||||||
pmf->write_multicol(*pmf_os);
|
|
||||||
|
|
||||||
// In dimension higher than 2, dx is easier to handle and visualize
|
|
||||||
if (num_variables() > 2) {
|
|
||||||
std::string pmf_dx_out_name = prefix + ".pmf.dx";
|
|
||||||
std::ostream *pmf_dx_os = cvm::proxy->output_stream(pmf_dx_out_name, mode);
|
|
||||||
if (!pmf_dx_os) return;
|
|
||||||
pmf->write_opendx(*pmf_dx_os);
|
|
||||||
*pmf_dx_os << std::endl;
|
|
||||||
cvm::proxy->close_output_stream(pmf_dx_out_name);
|
|
||||||
}
|
|
||||||
|
|
||||||
*pmf_os << std::endl;
|
|
||||||
cvm::proxy->close_output_stream(pmf_out_name);
|
|
||||||
}
|
}
|
||||||
|
|
||||||
if (b_CZAR_estimator) {
|
if (b_CZAR_estimator) {
|
||||||
// Write eABF CZAR-related quantities
|
// Write eABF CZAR-related quantities
|
||||||
|
write_grid_to_file<colvar_grid_count>(z_samples, prefix + ".zcount", close);
|
||||||
std::string z_samples_out_name = prefix + ".zcount";
|
|
||||||
|
|
||||||
std::ostream *z_samples_os =
|
|
||||||
cvm::proxy->output_stream(z_samples_out_name, mode);
|
|
||||||
if (!z_samples_os) return;
|
|
||||||
z_samples->write_multicol(*z_samples_os);
|
|
||||||
cvm::proxy->close_output_stream(z_samples_out_name);
|
|
||||||
|
|
||||||
if (b_czar_window_file) {
|
if (b_czar_window_file) {
|
||||||
std::string z_gradients_out_name = prefix + ".zgrad";
|
write_grid_to_file<colvar_grid_gradient>(z_gradients, prefix + ".zgrad", close);
|
||||||
|
|
||||||
std::ostream *z_gradients_os =
|
|
||||||
cvm::proxy->output_stream(z_gradients_out_name, mode);
|
|
||||||
if (!z_gradients_os) return;
|
|
||||||
z_gradients->write_multicol(*z_gradients_os);
|
|
||||||
cvm::proxy->close_output_stream(z_gradients_out_name);
|
|
||||||
}
|
}
|
||||||
|
|
||||||
// Calculate CZAR estimator of gradients
|
// Calculate CZAR estimator of gradients
|
||||||
@ -657,39 +650,15 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
|
|||||||
- cvm::temperature() * cvm::boltzmann() * z_samples->log_gradient_finite_diff(ix, n), n);
|
- cvm::temperature() * cvm::boltzmann() * z_samples->log_gradient_finite_diff(ix, n), n);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
write_grid_to_file<colvar_grid_gradient>(czar_gradients, prefix + ".czar.grad", close);
|
||||||
std::string czar_gradients_out_name = prefix + ".czar.grad";
|
|
||||||
|
|
||||||
std::ostream *czar_gradients_os =
|
|
||||||
cvm::proxy->output_stream(czar_gradients_out_name, mode);
|
|
||||||
if (!czar_gradients_os) return;
|
|
||||||
czar_gradients->write_multicol(*czar_gradients_os);
|
|
||||||
cvm::proxy->close_output_stream(czar_gradients_out_name);
|
|
||||||
|
|
||||||
if (b_integrate) {
|
if (b_integrate) {
|
||||||
// Do numerical integration (to high precision) and output a PMF
|
// Do numerical integration (to high precision) and output a PMF
|
||||||
cvm::real err;
|
cvm::real err;
|
||||||
czar_pmf->set_div();
|
czar_pmf->set_div();
|
||||||
czar_pmf->integrate(integrate_initial_iterations, integrate_initial_tol, err);
|
czar_pmf->integrate(integrate_iterations, integrate_tol, err);
|
||||||
czar_pmf->set_zero_minimum();
|
czar_pmf->set_zero_minimum();
|
||||||
|
write_grid_to_file<colvar_grid_scalar>(czar_pmf, prefix + ".czar.pmf", close);
|
||||||
std::string czar_pmf_out_name = prefix + ".czar.pmf";
|
|
||||||
std::ostream *czar_pmf_os = cvm::proxy->output_stream(czar_pmf_out_name, mode);
|
|
||||||
if (!czar_pmf_os) return;
|
|
||||||
czar_pmf->write_multicol(*czar_pmf_os);
|
|
||||||
|
|
||||||
// In dimension higher than 2, dx is easier to handle and visualize
|
|
||||||
if (num_variables() > 2) {
|
|
||||||
std::string czar_pmf_dx_out_name = prefix + ".czar.pmf.dx";
|
|
||||||
std::ostream *czar_pmf_dx_os = cvm::proxy->output_stream(czar_pmf_dx_out_name, mode);
|
|
||||||
if (!czar_pmf_dx_os) return;
|
|
||||||
czar_pmf->write_opendx(*czar_pmf_dx_os);
|
|
||||||
*czar_pmf_dx_os << std::endl;
|
|
||||||
cvm::proxy->close_output_stream(czar_pmf_dx_out_name);
|
|
||||||
}
|
|
||||||
|
|
||||||
*czar_pmf_os << std::endl;
|
|
||||||
cvm::proxy->close_output_stream(czar_pmf_out_name);
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
return;
|
return;
|
||||||
@ -836,25 +805,56 @@ std::istream & colvarbias_abf::read_state_data(std::istream& is)
|
|||||||
return is;
|
return is;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
int colvarbias_abf::write_output_files()
|
int colvarbias_abf::write_output_files()
|
||||||
{
|
{
|
||||||
|
if (cvm::debug()) {
|
||||||
|
cvm::log("ABF bias trying to write gradients and samples to disk");
|
||||||
|
}
|
||||||
|
|
||||||
|
if (shared_on && cvm::main()->proxy->replica_index() > 0) {
|
||||||
|
// No need to report the same data as replica 0, let it do the I/O job
|
||||||
|
return COLVARS_OK;
|
||||||
|
}
|
||||||
|
|
||||||
write_gradients_samples(output_prefix);
|
write_gradients_samples(output_prefix);
|
||||||
|
if (b_history_files) {
|
||||||
|
if ((cvm::step_absolute() % history_freq) == 0) {
|
||||||
|
write_gradients_samples(output_prefix + ".hist", false);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (b_UI_estimator) {
|
||||||
|
eabf_UI.calc_pmf();
|
||||||
|
eabf_UI.write_files();
|
||||||
|
}
|
||||||
|
|
||||||
return COLVARS_OK;
|
return COLVARS_OK;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
int colvarbias_abf::calc_energy(std::vector<colvarvalue> const *values)
|
int colvarbias_abf::calc_energy(std::vector<colvarvalue> const *values)
|
||||||
{
|
{
|
||||||
if (values) {
|
bias_energy = 0.0; // default value, overridden if a value can be calculated
|
||||||
return cvm::error("colvarbias_abf::calc_energy() with an argument "
|
|
||||||
"is currently not implemented.\n",
|
|
||||||
COLVARS_NOT_IMPLEMENTED);
|
|
||||||
}
|
|
||||||
|
|
||||||
if (num_variables() != 1) return 0.0;
|
if (num_variables() > 1 || values != NULL) {
|
||||||
|
// Use simple estimate: neglect effect of fullSamples,
|
||||||
|
// return value at center of bin
|
||||||
|
if (pmf != NULL) {
|
||||||
|
std::vector<int> const curr_bin = values ?
|
||||||
|
pmf->get_colvars_index(*values) :
|
||||||
|
pmf->get_colvars_index();
|
||||||
|
|
||||||
|
if (pmf->index_ok(curr_bin)) {
|
||||||
|
bias_energy = pmf->value(curr_bin);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return COLVARS_OK;
|
||||||
|
}
|
||||||
|
|
||||||
// Get the home bin.
|
// Get the home bin.
|
||||||
int home0 = gradients->current_bin_scalar(0);
|
int home0 = gradients->current_bin_scalar(0);
|
||||||
if (home0 < 0) return 0.0;
|
if (home0 < 0) return COLVARS_OK;
|
||||||
int gradient_len = (int)(gradients->number_of_points(0));
|
int gradient_len = (int)(gradients->number_of_points(0));
|
||||||
int home = (home0 < gradient_len) ? home0 : (gradient_len-1);
|
int home = (home0 < gradient_len) ? home0 : (gradient_len-1);
|
||||||
|
|
||||||
@ -886,5 +886,6 @@ int colvarbias_abf::calc_energy(std::vector<colvarvalue> const *values)
|
|||||||
sum += fact*gradients->value(ix)/count*gradients->widths[0]*frac;
|
sum += fact*gradients->value(ix)/count*gradients->widths[0]*frac;
|
||||||
|
|
||||||
// The applied potential is the negative integral of force samples.
|
// The applied potential is the negative integral of force samples.
|
||||||
return -sum;
|
bias_energy = -sum;
|
||||||
|
return COLVARS_OK;
|
||||||
}
|
}
|
||||||
|
|||||||
@ -15,6 +15,7 @@
|
|||||||
#include <sstream>
|
#include <sstream>
|
||||||
#include <iomanip>
|
#include <iomanip>
|
||||||
|
|
||||||
|
#include "colvarproxy.h"
|
||||||
#include "colvarbias.h"
|
#include "colvarbias.h"
|
||||||
#include "colvargrid.h"
|
#include "colvargrid.h"
|
||||||
#include "colvar_UIestimator.h"
|
#include "colvar_UIestimator.h"
|
||||||
@ -56,8 +57,6 @@ private:
|
|||||||
size_t full_samples;
|
size_t full_samples;
|
||||||
/// Number of samples per bin before applying a scaled-down biasing force
|
/// Number of samples per bin before applying a scaled-down biasing force
|
||||||
size_t min_samples;
|
size_t min_samples;
|
||||||
/// frequency for updating output files
|
|
||||||
int output_freq;
|
|
||||||
/// Write combined files with a history of all output data?
|
/// Write combined files with a history of all output data?
|
||||||
bool b_history_files;
|
bool b_history_files;
|
||||||
/// Write CZAR output file for stratified eABF (.zgrad)
|
/// Write CZAR output file for stratified eABF (.zgrad)
|
||||||
@ -74,13 +73,13 @@ private:
|
|||||||
/// Frequency for updating pABF PMF (if zero, pABF is not used)
|
/// Frequency for updating pABF PMF (if zero, pABF is not used)
|
||||||
int pabf_freq;
|
int pabf_freq;
|
||||||
/// Max number of CG iterations for integrating PMF at startup and for file output
|
/// Max number of CG iterations for integrating PMF at startup and for file output
|
||||||
int integrate_initial_iterations;
|
|
||||||
/// Tolerance for integrating PMF at startup and for file output
|
|
||||||
cvm::real integrate_initial_tol;
|
|
||||||
/// Max number of CG iterations for integrating PMF at on-the-fly pABF updates
|
|
||||||
int integrate_iterations;
|
int integrate_iterations;
|
||||||
/// Tolerance for integrating PMF at on-the-fly pABF updates
|
/// Tolerance for integrating PMF at startup and for file output
|
||||||
cvm::real integrate_tol;
|
cvm::real integrate_tol;
|
||||||
|
/// Max number of CG iterations for integrating PMF at on-the-fly pABF updates
|
||||||
|
int pabf_integrate_iterations;
|
||||||
|
/// Tolerance for integrating PMF at on-the-fly pABF updates
|
||||||
|
cvm::real pabf_integrate_tol;
|
||||||
|
|
||||||
/// Cap the biasing force to be applied? (option maxForce)
|
/// Cap the biasing force to be applied? (option maxForce)
|
||||||
bool cap_force;
|
bool cap_force;
|
||||||
@ -151,11 +150,16 @@ private:
|
|||||||
virtual int bin_count(int bin_index);
|
virtual int bin_count(int bin_index);
|
||||||
|
|
||||||
/// Write human-readable FE gradients and sample count, and DX file in dim > 2
|
/// Write human-readable FE gradients and sample count, and DX file in dim > 2
|
||||||
void write_gradients_samples(const std::string &prefix, bool append = false);
|
void write_gradients_samples(const std::string &prefix, bool close = true);
|
||||||
|
|
||||||
/// Read human-readable FE gradients and sample count (if not using restart)
|
/// Read human-readable FE gradients and sample count (if not using restart)
|
||||||
void read_gradients_samples();
|
void read_gradients_samples();
|
||||||
|
|
||||||
|
/// Template used in write_gradient_samples()
|
||||||
|
template <class T> int write_grid_to_file(T const *grid,
|
||||||
|
std::string const &name,
|
||||||
|
bool close);
|
||||||
|
|
||||||
virtual std::istream& read_state_data(std::istream&);
|
virtual std::istream& read_state_data(std::istream&);
|
||||||
virtual std::ostream& write_state_data(std::ostream&);
|
virtual std::ostream& write_state_data(std::ostream&);
|
||||||
virtual int write_output_files();
|
virtual int write_output_files();
|
||||||
|
|||||||
@ -30,9 +30,10 @@ int colvarbias_histogram::init(std::string const &conf)
|
|||||||
|
|
||||||
size_t i;
|
size_t i;
|
||||||
|
|
||||||
get_keyval(conf, "outputFile", out_name, std::string(""));
|
get_keyval(conf, "outputFile", out_name, "");
|
||||||
get_keyval(conf, "outputFileDX", out_name_dx, std::string(""));
|
// Write DX file by default only in dimension >= 3
|
||||||
get_keyval(conf, "outputFreq", output_freq, cvm::restart_out_freq);
|
std::string default_name_dx = this->num_variables() > 2 ? "" : "none";
|
||||||
|
get_keyval(conf, "outputFileDX", out_name_dx, default_name_dx);
|
||||||
|
|
||||||
/// with VMD, this may not be an error
|
/// with VMD, this may not be an error
|
||||||
// if ( output_freq == 0 ) {
|
// if ( output_freq == 0 ) {
|
||||||
@ -146,9 +147,11 @@ int colvarbias_histogram::update()
|
|||||||
bin[i] = grid->current_bin_scalar(i);
|
bin[i] = grid->current_bin_scalar(i);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
if (can_accumulate_data()) {
|
||||||
if (grid->index_ok(bin)) {
|
if (grid->index_ok(bin)) {
|
||||||
grid->acc_value(bin, 1.0);
|
grid->acc_value(bin, 1.0);
|
||||||
}
|
}
|
||||||
|
}
|
||||||
} else {
|
} else {
|
||||||
// update indices for vector/array values
|
// update indices for vector/array values
|
||||||
size_t iv, i;
|
size_t iv, i;
|
||||||
@ -163,10 +166,6 @@ int colvarbias_histogram::update()
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
if (output_freq && (cvm::step_absolute() % output_freq) == 0) {
|
|
||||||
write_output_files();
|
|
||||||
}
|
|
||||||
|
|
||||||
error_code |= cvm::get_error();
|
error_code |= cvm::get_error();
|
||||||
return error_code;
|
return error_code;
|
||||||
}
|
}
|
||||||
@ -179,7 +178,7 @@ int colvarbias_histogram::write_output_files()
|
|||||||
return COLVARS_OK;
|
return COLVARS_OK;
|
||||||
}
|
}
|
||||||
|
|
||||||
if (out_name.size()) {
|
if (out_name.size() && out_name != "none") {
|
||||||
cvm::log("Writing the histogram file \""+out_name+"\".\n");
|
cvm::log("Writing the histogram file \""+out_name+"\".\n");
|
||||||
cvm::backup_file(out_name.c_str());
|
cvm::backup_file(out_name.c_str());
|
||||||
std::ostream *grid_os = cvm::proxy->output_stream(out_name);
|
std::ostream *grid_os = cvm::proxy->output_stream(out_name);
|
||||||
@ -191,7 +190,7 @@ int colvarbias_histogram::write_output_files()
|
|||||||
cvm::proxy->close_output_stream(out_name);
|
cvm::proxy->close_output_stream(out_name);
|
||||||
}
|
}
|
||||||
|
|
||||||
if (out_name_dx.size()) {
|
if (out_name_dx.size() && out_name_dx != "none") {
|
||||||
cvm::log("Writing the histogram file \""+out_name_dx+"\".\n");
|
cvm::log("Writing the histogram file \""+out_name_dx+"\".\n");
|
||||||
cvm::backup_file(out_name_dx.c_str());
|
cvm::backup_file(out_name_dx.c_str());
|
||||||
std::ostream *grid_os = cvm::proxy->output_stream(out_name_dx);
|
std::ostream *grid_os = cvm::proxy->output_stream(out_name_dx);
|
||||||
|
|||||||
@ -566,8 +566,8 @@ int colvarbias_meta::update_grid_params()
|
|||||||
int colvarbias_meta::update_bias()
|
int colvarbias_meta::update_bias()
|
||||||
{
|
{
|
||||||
// add a new hill if the required time interval has passed
|
// add a new hill if the required time interval has passed
|
||||||
if ((cvm::step_absolute() % new_hill_freq) == 0 &&
|
if (((cvm::step_absolute() % new_hill_freq) == 0) &&
|
||||||
is_enabled(f_cvb_history_dependent)) {
|
can_accumulate_data() && is_enabled(f_cvb_history_dependent)) {
|
||||||
|
|
||||||
if (cvm::debug()) {
|
if (cvm::debug()) {
|
||||||
cvm::log("Metadynamics bias \""+this->name+"\""+
|
cvm::log("Metadynamics bias \""+this->name+"\""+
|
||||||
@ -883,7 +883,7 @@ void colvarbias_meta::project_hills(colvarbias_meta::hill_iter h_first,
|
|||||||
|
|
||||||
// TODO: improve it by looping over a small subgrid instead of the whole grid
|
// TODO: improve it by looping over a small subgrid instead of the whole grid
|
||||||
|
|
||||||
std::vector<colvarvalue> colvar_values(num_variables());
|
std::vector<colvarvalue> new_colvar_values(num_variables());
|
||||||
std::vector<cvm::real> colvar_forces_scalar(num_variables());
|
std::vector<cvm::real> colvar_forces_scalar(num_variables());
|
||||||
|
|
||||||
std::vector<int> he_ix = he->new_index();
|
std::vector<int> he_ix = he->new_index();
|
||||||
@ -902,17 +902,17 @@ void colvarbias_meta::project_hills(colvarbias_meta::hill_iter h_first,
|
|||||||
count++) {
|
count++) {
|
||||||
size_t i;
|
size_t i;
|
||||||
for (i = 0; i < num_variables(); i++) {
|
for (i = 0; i < num_variables(); i++) {
|
||||||
colvar_values[i] = hills_energy->bin_to_value_scalar(he_ix[i], i);
|
new_colvar_values[i] = hills_energy->bin_to_value_scalar(he_ix[i], i);
|
||||||
}
|
}
|
||||||
|
|
||||||
// loop over the hills and increment the energy grid locally
|
// loop over the hills and increment the energy grid locally
|
||||||
hills_energy_here = 0.0;
|
hills_energy_here = 0.0;
|
||||||
calc_hills(h_first, h_last, hills_energy_here, &colvar_values);
|
calc_hills(h_first, h_last, hills_energy_here, &new_colvar_values);
|
||||||
he->acc_value(he_ix, hills_energy_here);
|
he->acc_value(he_ix, hills_energy_here);
|
||||||
|
|
||||||
for (i = 0; i < num_variables(); i++) {
|
for (i = 0; i < num_variables(); i++) {
|
||||||
hills_forces_here[i].reset();
|
hills_forces_here[i].reset();
|
||||||
calc_hills_force(i, h_first, h_last, hills_forces_here, &colvar_values);
|
calc_hills_force(i, h_first, h_last, hills_forces_here, &new_colvar_values);
|
||||||
colvar_forces_scalar[i] = hills_forces_here[i].real_value;
|
colvar_forces_scalar[i] = hills_forces_here[i].real_value;
|
||||||
}
|
}
|
||||||
hg->acc_force(hg_ix, &(colvar_forces_scalar.front()));
|
hg->acc_force(hg_ix, &(colvar_forces_scalar.front()));
|
||||||
@ -935,16 +935,18 @@ void colvarbias_meta::project_hills(colvarbias_meta::hill_iter h_first,
|
|||||||
|
|
||||||
} else {
|
} else {
|
||||||
|
|
||||||
|
// TODO delete this (never used)
|
||||||
|
|
||||||
// simpler version, with just the energy
|
// simpler version, with just the energy
|
||||||
|
|
||||||
for ( ; (he->index_ok(he_ix)); ) {
|
for ( ; (he->index_ok(he_ix)); ) {
|
||||||
|
|
||||||
for (size_t i = 0; i < num_variables(); i++) {
|
for (size_t i = 0; i < num_variables(); i++) {
|
||||||
colvar_values[i] = hills_energy->bin_to_value_scalar(he_ix[i], i);
|
new_colvar_values[i] = hills_energy->bin_to_value_scalar(he_ix[i], i);
|
||||||
}
|
}
|
||||||
|
|
||||||
hills_energy_here = 0.0;
|
hills_energy_here = 0.0;
|
||||||
calc_hills(h_first, h_last, hills_energy_here, &colvar_values);
|
calc_hills(h_first, h_last, hills_energy_here, &new_colvar_values);
|
||||||
he->acc_value(he_ix, hills_energy_here);
|
he->acc_value(he_ix, hills_energy_here);
|
||||||
|
|
||||||
he->incr(he_ix);
|
he->incr(he_ix);
|
||||||
@ -1240,7 +1242,7 @@ void colvarbias_meta::read_replica_files()
|
|||||||
|
|
||||||
// test whether this is the end of the file
|
// test whether this is the end of the file
|
||||||
is.seekg(0, std::ios::end);
|
is.seekg(0, std::ios::end);
|
||||||
if (is.tellg() > (replicas[ir])->replica_hills_file_pos+1) {
|
if (is.tellg() > (replicas[ir])->replica_hills_file_pos + ((std::streampos) 1)) {
|
||||||
(replicas[ir])->update_status++;
|
(replicas[ir])->update_status++;
|
||||||
} else {
|
} else {
|
||||||
(replicas[ir])->update_status = 0;
|
(replicas[ir])->update_status = 0;
|
||||||
@ -1324,7 +1326,7 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is)
|
|||||||
hills_energy_gradients = new colvar_grid_gradient(colvars);
|
hills_energy_gradients = new colvar_grid_gradient(colvars);
|
||||||
}
|
}
|
||||||
|
|
||||||
size_t const hills_energy_pos = is.tellg();
|
std::streampos const hills_energy_pos = is.tellg();
|
||||||
std::string key;
|
std::string key;
|
||||||
if (!(is >> key)) {
|
if (!(is >> key)) {
|
||||||
if (hills_energy_backup != NULL) {
|
if (hills_energy_backup != NULL) {
|
||||||
@ -1363,7 +1365,7 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is)
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
size_t const hills_energy_gradients_pos = is.tellg();
|
std::streampos const hills_energy_gradients_pos = is.tellg();
|
||||||
if (!(is >> key)) {
|
if (!(is >> key)) {
|
||||||
if (hills_energy_backup != NULL) {
|
if (hills_energy_backup != NULL) {
|
||||||
delete hills_energy;
|
delete hills_energy;
|
||||||
@ -1511,7 +1513,7 @@ std::istream & colvarbias_meta::read_hill(std::istream &is)
|
|||||||
{
|
{
|
||||||
if (!is) return is; // do nothing if failbit is set
|
if (!is) return is; // do nothing if failbit is set
|
||||||
|
|
||||||
size_t const start_pos = is.tellg();
|
std::streampos const start_pos = is.tellg();
|
||||||
size_t i = 0;
|
size_t i = 0;
|
||||||
|
|
||||||
std::string data;
|
std::string data;
|
||||||
@ -1958,11 +1960,12 @@ colvarbias_meta::hill::hill(cvm::step_number it_in,
|
|||||||
|
|
||||||
|
|
||||||
colvarbias_meta::hill::hill(colvarbias_meta::hill const &h)
|
colvarbias_meta::hill::hill(colvarbias_meta::hill const &h)
|
||||||
: sW(1.0),
|
: it(h.it),
|
||||||
|
hill_value(0.0),
|
||||||
|
sW(1.0),
|
||||||
W(h.W),
|
W(h.W),
|
||||||
centers(h.centers),
|
centers(h.centers),
|
||||||
sigmas(h.sigmas),
|
sigmas(h.sigmas),
|
||||||
it(h.it),
|
|
||||||
replica(h.replica)
|
replica(h.replica)
|
||||||
{}
|
{}
|
||||||
|
|
||||||
|
|||||||
@ -257,7 +257,7 @@ protected:
|
|||||||
std::string replica_hills_file;
|
std::string replica_hills_file;
|
||||||
|
|
||||||
/// Position within replica_hills_file (when reading it)
|
/// Position within replica_hills_file (when reading it)
|
||||||
int replica_hills_file_pos;
|
std::streampos replica_hills_file_pos;
|
||||||
|
|
||||||
};
|
};
|
||||||
|
|
||||||
|
|||||||
@ -169,7 +169,7 @@ cvm::atom_group *colvar::cvc::parse_group(std::string const &conf,
|
|||||||
group->check_keywords(group_conf, group_key);
|
group->check_keywords(group_conf, group_key);
|
||||||
if (cvm::get_error()) {
|
if (cvm::get_error()) {
|
||||||
cvm::error("Error parsing definition for atom group \""+
|
cvm::error("Error parsing definition for atom group \""+
|
||||||
std::string(group_key)+"\"\n.", INPUT_ERROR);
|
std::string(group_key)+"\".", INPUT_ERROR);
|
||||||
}
|
}
|
||||||
cvm::decrease_depth();
|
cvm::decrease_depth();
|
||||||
|
|
||||||
@ -200,40 +200,40 @@ int colvar::cvc::init_dependencies() {
|
|||||||
|
|
||||||
init_feature(f_cvc_periodic, "periodic", f_type_static);
|
init_feature(f_cvc_periodic, "periodic", f_type_static);
|
||||||
|
|
||||||
init_feature(f_cvc_width, "defined width", f_type_static);
|
init_feature(f_cvc_width, "defined_width", f_type_static);
|
||||||
|
|
||||||
init_feature(f_cvc_lower_boundary, "defined lower boundary", f_type_static);
|
init_feature(f_cvc_lower_boundary, "defined_lower_boundary", f_type_static);
|
||||||
|
|
||||||
init_feature(f_cvc_upper_boundary, "defined upper boundary", f_type_static);
|
init_feature(f_cvc_upper_boundary, "defined_upper_boundary", f_type_static);
|
||||||
|
|
||||||
init_feature(f_cvc_gradient, "gradient", f_type_dynamic);
|
init_feature(f_cvc_gradient, "gradient", f_type_dynamic);
|
||||||
|
|
||||||
init_feature(f_cvc_explicit_gradient, "explicit gradient", f_type_static);
|
init_feature(f_cvc_explicit_gradient, "explicit_gradient", f_type_static);
|
||||||
require_feature_children(f_cvc_explicit_gradient, f_ag_explicit_gradient);
|
require_feature_children(f_cvc_explicit_gradient, f_ag_explicit_gradient);
|
||||||
|
|
||||||
init_feature(f_cvc_inv_gradient, "inverse gradient", f_type_dynamic);
|
init_feature(f_cvc_inv_gradient, "inverse_gradient", f_type_dynamic);
|
||||||
require_feature_self(f_cvc_inv_gradient, f_cvc_gradient);
|
require_feature_self(f_cvc_inv_gradient, f_cvc_gradient);
|
||||||
|
|
||||||
init_feature(f_cvc_debug_gradient, "debug gradient", f_type_user);
|
init_feature(f_cvc_debug_gradient, "debug_gradient", f_type_user);
|
||||||
require_feature_self(f_cvc_debug_gradient, f_cvc_gradient);
|
require_feature_self(f_cvc_debug_gradient, f_cvc_gradient);
|
||||||
require_feature_self(f_cvc_debug_gradient, f_cvc_explicit_gradient);
|
require_feature_self(f_cvc_debug_gradient, f_cvc_explicit_gradient);
|
||||||
|
|
||||||
init_feature(f_cvc_Jacobian, "Jacobian derivative", f_type_dynamic);
|
init_feature(f_cvc_Jacobian, "Jacobian_derivative", f_type_dynamic);
|
||||||
require_feature_self(f_cvc_Jacobian, f_cvc_inv_gradient);
|
require_feature_self(f_cvc_Jacobian, f_cvc_inv_gradient);
|
||||||
|
|
||||||
// Compute total force on first site only to avoid unwanted
|
// Compute total force on first site only to avoid unwanted
|
||||||
// coupling to other colvars (see e.g. Ciccotti et al., 2005)
|
// coupling to other colvars (see e.g. Ciccotti et al., 2005)
|
||||||
init_feature(f_cvc_one_site_total_force, "compute total force from one group", f_type_user);
|
init_feature(f_cvc_one_site_total_force, "total_force_from_one_group", f_type_user);
|
||||||
require_feature_self(f_cvc_one_site_total_force, f_cvc_com_based);
|
require_feature_self(f_cvc_one_site_total_force, f_cvc_com_based);
|
||||||
|
|
||||||
init_feature(f_cvc_com_based, "depends on group centers of mass", f_type_static);
|
init_feature(f_cvc_com_based, "function_of_centers_of_mass", f_type_static);
|
||||||
|
|
||||||
init_feature(f_cvc_pbc_minimum_image, "use minimum-image distances with PBCs", f_type_user);
|
init_feature(f_cvc_pbc_minimum_image, "use_minimum-image_with_PBCs", f_type_user);
|
||||||
|
|
||||||
init_feature(f_cvc_scalable, "scalable calculation", f_type_static);
|
init_feature(f_cvc_scalable, "scalable_calculation", f_type_static);
|
||||||
require_feature_self(f_cvc_scalable, f_cvc_scalable_com);
|
require_feature_self(f_cvc_scalable, f_cvc_scalable_com);
|
||||||
|
|
||||||
init_feature(f_cvc_scalable_com, "scalable calculation of centers of mass", f_type_static);
|
init_feature(f_cvc_scalable_com, "scalable_calculation_of_centers_of_mass", f_type_static);
|
||||||
require_feature_self(f_cvc_scalable_com, f_cvc_com_based);
|
require_feature_self(f_cvc_scalable_com, f_cvc_com_based);
|
||||||
|
|
||||||
|
|
||||||
@ -626,6 +626,7 @@ void colvar::cvc::wrap(colvarvalue & /* x_unwrapped */) const
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
// Static members
|
// Static members
|
||||||
|
|
||||||
std::vector<colvardeps::feature *> colvar::cvc::cvc_features;
|
std::vector<colvardeps::feature *> colvar::cvc::cvc_features;
|
||||||
|
|||||||
@ -1358,8 +1358,14 @@ protected:
|
|||||||
cvm::atom_group *atoms;
|
cvm::atom_group *atoms;
|
||||||
|
|
||||||
/// Reference coordinates (for RMSD calculation only)
|
/// Reference coordinates (for RMSD calculation only)
|
||||||
|
/// Includes sets with symmetry permutations (n_permutations * n_atoms)
|
||||||
std::vector<cvm::atom_pos> ref_pos;
|
std::vector<cvm::atom_pos> ref_pos;
|
||||||
|
|
||||||
|
/// Number of permutations of symmetry-related atoms
|
||||||
|
size_t n_permutations;
|
||||||
|
|
||||||
|
/// Index of the permutation yielding the smallest RMSD (0 for identity)
|
||||||
|
size_t best_perm_index;
|
||||||
public:
|
public:
|
||||||
|
|
||||||
/// Constructor
|
/// Constructor
|
||||||
@ -1661,6 +1667,33 @@ public:
|
|||||||
|
|
||||||
#endif // C++11 checking
|
#endif // C++11 checking
|
||||||
|
|
||||||
|
|
||||||
|
// \brief Colvar component: total value of a scalar map
|
||||||
|
// (usually implemented as a grid by the simulation engine)
|
||||||
|
class colvar::map_total
|
||||||
|
: public colvar::cvc
|
||||||
|
{
|
||||||
|
public:
|
||||||
|
|
||||||
|
map_total();
|
||||||
|
map_total(std::string const &conf);
|
||||||
|
virtual ~map_total() {}
|
||||||
|
virtual int init(std::string const &conf);
|
||||||
|
virtual void calc_value();
|
||||||
|
virtual void calc_gradients();
|
||||||
|
virtual void apply_force(colvarvalue const &force);
|
||||||
|
|
||||||
|
protected:
|
||||||
|
|
||||||
|
/// Identifier of the map object (as used by the simulation engine)
|
||||||
|
std::string map_name;
|
||||||
|
|
||||||
|
/// Index of the map objet in the proxy arrays
|
||||||
|
int volmap_index;
|
||||||
|
};
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
// metrics functions for cvc implementations
|
// metrics functions for cvc implementations
|
||||||
|
|
||||||
// simple definitions of the distance functions; these are useful only
|
// simple definitions of the distance functions; these are useful only
|
||||||
@ -1691,6 +1724,6 @@ public:
|
|||||||
{ \
|
{ \
|
||||||
return this->dist2_lgrad(x2, x1); \
|
return this->dist2_lgrad(x2, x1); \
|
||||||
} \
|
} \
|
||||||
\
|
|
||||||
|
|
||||||
#endif
|
#endif
|
||||||
|
|||||||
@ -7,6 +7,8 @@
|
|||||||
// If you wish to distribute your changes, please submit them to the
|
// If you wish to distribute your changes, please submit them to the
|
||||||
// Colvars repository at GitHub.
|
// Colvars repository at GitHub.
|
||||||
|
|
||||||
|
#include <algorithm>
|
||||||
|
|
||||||
#include "colvarmodule.h"
|
#include "colvarmodule.h"
|
||||||
#include "colvarvalue.h"
|
#include "colvarvalue.h"
|
||||||
#include "colvarparse.h"
|
#include "colvarparse.h"
|
||||||
@ -1045,6 +1047,44 @@ colvar::rmsd::rmsd(std::string const &conf)
|
|||||||
// this is only required for ABF, but we do both groups here for better caching
|
// this is only required for ABF, but we do both groups here for better caching
|
||||||
atoms->rot.request_group2_gradients(atoms->size());
|
atoms->rot.request_group2_gradients(atoms->size());
|
||||||
}
|
}
|
||||||
|
|
||||||
|
std::string perm_conf;
|
||||||
|
size_t pos = 0; // current position in config string
|
||||||
|
n_permutations = 1;
|
||||||
|
|
||||||
|
while (key_lookup(conf, "atomPermutation", &perm_conf, &pos)) {
|
||||||
|
std::vector<size_t> perm;
|
||||||
|
if (perm_conf.size()) {
|
||||||
|
std::istringstream is(perm_conf);
|
||||||
|
size_t index;
|
||||||
|
while (is >> index) {
|
||||||
|
std::vector<int> const &ids = atoms->ids();
|
||||||
|
size_t const ia = std::find(ids.begin(), ids.end(), index-1) - ids.begin();
|
||||||
|
if (ia == atoms->size()) {
|
||||||
|
cvm::error("Error: atom id " + cvm::to_str(index) +
|
||||||
|
" is not a member of group \"atoms\".");
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
if (std::find(perm.begin(), perm.end(), ia) != perm.end()) {
|
||||||
|
cvm::error("Error: atom id " + cvm::to_str(index) +
|
||||||
|
" is mentioned more than once in atomPermutation list.");
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
perm.push_back(ia);
|
||||||
|
}
|
||||||
|
if (perm.size() != atoms->size()) {
|
||||||
|
cvm::error("Error: symmetry permutation in input contains " + cvm::to_str(perm.size()) +
|
||||||
|
" indices, but group \"atoms\" contains " + cvm::to_str(atoms->size()) + " atoms.");
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
cvm::log("atomPermutation = " + cvm::to_str(perm));
|
||||||
|
n_permutations++;
|
||||||
|
// Record a copy of reference positions in new order
|
||||||
|
for (size_t ia = 0; ia < atoms->size(); ia++) {
|
||||||
|
ref_pos.push_back(ref_pos[perm[ia]]);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
@ -1056,6 +1096,20 @@ void colvar::rmsd::calc_value()
|
|||||||
for (size_t ia = 0; ia < atoms->size(); ia++) {
|
for (size_t ia = 0; ia < atoms->size(); ia++) {
|
||||||
x.real_value += ((*atoms)[ia].pos - ref_pos[ia]).norm2();
|
x.real_value += ((*atoms)[ia].pos - ref_pos[ia]).norm2();
|
||||||
}
|
}
|
||||||
|
best_perm_index = 0;
|
||||||
|
|
||||||
|
// Compute sum of squares for each symmetry permutation of atoms, keep the smallest
|
||||||
|
size_t ref_pos_index = atoms->size();
|
||||||
|
for (size_t ip = 1; ip < n_permutations; ip++) {
|
||||||
|
cvm::real value = 0.0;
|
||||||
|
for (size_t ia = 0; ia < atoms->size(); ia++) {
|
||||||
|
value += ((*atoms)[ia].pos - ref_pos[ref_pos_index++]).norm2();
|
||||||
|
}
|
||||||
|
if (value < x.real_value) {
|
||||||
|
x.real_value = value;
|
||||||
|
best_perm_index = ip;
|
||||||
|
}
|
||||||
|
}
|
||||||
x.real_value /= cvm::real(atoms->size()); // MSD
|
x.real_value /= cvm::real(atoms->size()); // MSD
|
||||||
x.real_value = cvm::sqrt(x.real_value);
|
x.real_value = cvm::sqrt(x.real_value);
|
||||||
}
|
}
|
||||||
@ -1067,8 +1121,10 @@ void colvar::rmsd::calc_gradients()
|
|||||||
0.5 / (x.real_value * cvm::real(atoms->size())) :
|
0.5 / (x.real_value * cvm::real(atoms->size())) :
|
||||||
0.0;
|
0.0;
|
||||||
|
|
||||||
|
// Use the appropriate symmetry permutation of reference positions to calculate gradients
|
||||||
|
size_t const start = atoms->size() * best_perm_index;
|
||||||
for (size_t ia = 0; ia < atoms->size(); ia++) {
|
for (size_t ia = 0; ia < atoms->size(); ia++) {
|
||||||
(*atoms)[ia].grad = (drmsddx2 * 2.0 * ((*atoms)[ia].pos - ref_pos[ia]));
|
(*atoms)[ia].grad = (drmsddx2 * 2.0 * ((*atoms)[ia].pos - ref_pos[start + ia]));
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
60
lib/colvars/colvarcomp_volmaps.cpp
Normal file
60
lib/colvars/colvarcomp_volmaps.cpp
Normal file
@ -0,0 +1,60 @@
|
|||||||
|
// -*- c++ -*-
|
||||||
|
|
||||||
|
// This file is part of the Collective Variables module (Colvars).
|
||||||
|
// The original version of Colvars and its updates are located at:
|
||||||
|
// https://github.com/Colvars/colvars
|
||||||
|
// Please update all Colvars source files before making any changes.
|
||||||
|
// If you wish to distribute your changes, please submit them to the
|
||||||
|
// Colvars repository at GitHub.
|
||||||
|
|
||||||
|
#include "colvarmodule.h"
|
||||||
|
#include "colvarvalue.h"
|
||||||
|
#include "colvarparse.h"
|
||||||
|
#include "colvar.h"
|
||||||
|
#include "colvarcomp.h"
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
colvar::map_total::map_total()
|
||||||
|
: cvc(), volmap_index(-1)
|
||||||
|
{
|
||||||
|
function_type = "map_total";
|
||||||
|
x.type(colvarvalue::type_scalar);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
colvar::map_total::map_total(std::string const &conf)
|
||||||
|
: cvc(), volmap_index(-1)
|
||||||
|
{
|
||||||
|
function_type = "map_total";
|
||||||
|
x.type(colvarvalue::type_scalar);
|
||||||
|
map_total::init(conf);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int colvar::map_total::init(std::string const &conf)
|
||||||
|
{
|
||||||
|
int error_code = cvc::init(conf);
|
||||||
|
get_keyval(conf, "mapName", map_name, map_name);
|
||||||
|
volmap_index = (cvm::proxy)->init_volmap(map_name);
|
||||||
|
error_code |= volmap_index > 0 ? COLVARS_OK : INPUT_ERROR;
|
||||||
|
return error_code;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
void colvar::map_total::calc_value()
|
||||||
|
{
|
||||||
|
x.real_value = (cvm::proxy)->get_volmap_value(volmap_index);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
void colvar::map_total::calc_gradients()
|
||||||
|
{
|
||||||
|
// Atomic coordinates are not available here
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
void colvar::map_total::apply_force(colvarvalue const &force)
|
||||||
|
{
|
||||||
|
(cvm::proxy)->apply_volmap_force(volmap_index, force.real_value);
|
||||||
|
}
|
||||||
@ -115,7 +115,9 @@ bool colvardeps::get_keyval_feature(colvarparse *cvp,
|
|||||||
}
|
}
|
||||||
bool value;
|
bool value;
|
||||||
bool const found = cvp->get_keyval(conf, key, value, def_value, parse_mode);
|
bool const found = cvp->get_keyval(conf, key, value, def_value, parse_mode);
|
||||||
if (value) enable(feature_id);
|
// If the default value is on, this function should be able to disable the feature!
|
||||||
|
set_enabled(feature_id, value);
|
||||||
|
|
||||||
return found;
|
return found;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
@ -227,6 +227,8 @@ public:
|
|||||||
f_cvb_active,
|
f_cvb_active,
|
||||||
/// \brief Bias is awake (active on its own accord) this timestep
|
/// \brief Bias is awake (active on its own accord) this timestep
|
||||||
f_cvb_awake,
|
f_cvb_awake,
|
||||||
|
/// Accumulates data starting from step 0 of a simulation run
|
||||||
|
f_cvb_step_zero_data,
|
||||||
/// \brief will apply forces
|
/// \brief will apply forces
|
||||||
f_cvb_apply_force,
|
f_cvb_apply_force,
|
||||||
/// \brief force this bias to act on actual value for extended-Lagrangian coordinates
|
/// \brief force this bias to act on actual value for extended-Lagrangian coordinates
|
||||||
@ -302,6 +304,10 @@ public:
|
|||||||
f_cv_hard_lower_boundary,
|
f_cv_hard_lower_boundary,
|
||||||
/// \brief The upper boundary is not defined from user's choice
|
/// \brief The upper boundary is not defined from user's choice
|
||||||
f_cv_hard_upper_boundary,
|
f_cv_hard_upper_boundary,
|
||||||
|
/// \brief Reflecting lower boundary condition
|
||||||
|
f_cv_reflecting_lower_boundary,
|
||||||
|
/// \brief Reflecting upper boundary condition
|
||||||
|
f_cv_reflecting_upper_boundary,
|
||||||
/// \brief Provide a discretization of the values of the colvar to
|
/// \brief Provide a discretization of the values of the colvar to
|
||||||
/// be used by the biases or in analysis (needs lower and upper
|
/// be used by the biases or in analysis (needs lower and upper
|
||||||
/// boundary)
|
/// boundary)
|
||||||
|
|||||||
@ -239,19 +239,21 @@ public:
|
|||||||
}
|
}
|
||||||
|
|
||||||
/// \brief Constructor from a vector of colvars
|
/// \brief Constructor from a vector of colvars
|
||||||
|
/// \param add_extra_bin requests that non-periodic dimensions are extended
|
||||||
|
/// by 1 bin to accommodate the integral (PMF) of another gridded quantity (gradient)
|
||||||
colvar_grid(std::vector<colvar *> const &colvars,
|
colvar_grid(std::vector<colvar *> const &colvars,
|
||||||
T const &t = T(),
|
T const &t = T(),
|
||||||
size_t mult_i = 1,
|
size_t mult_i = 1,
|
||||||
bool margin = false)
|
bool add_extra_bin = false)
|
||||||
: has_data(false)
|
: has_data(false)
|
||||||
{
|
{
|
||||||
this->init_from_colvars(colvars, t, mult_i, margin);
|
this->init_from_colvars(colvars, t, mult_i, add_extra_bin);
|
||||||
}
|
}
|
||||||
|
|
||||||
int init_from_colvars(std::vector<colvar *> const &colvars,
|
int init_from_colvars(std::vector<colvar *> const &colvars,
|
||||||
T const &t = T(),
|
T const &t = T(),
|
||||||
size_t mult_i = 1,
|
size_t mult_i = 1,
|
||||||
bool margin = false)
|
bool add_extra_bin = false)
|
||||||
{
|
{
|
||||||
if (cvm::debug()) {
|
if (cvm::debug()) {
|
||||||
cvm::log("Reading grid configuration from collective variables.\n");
|
cvm::log("Reading grid configuration from collective variables.\n");
|
||||||
@ -299,7 +301,7 @@ public:
|
|||||||
use_actual_value[i-1] = true;
|
use_actual_value[i-1] = true;
|
||||||
}
|
}
|
||||||
|
|
||||||
if (margin) {
|
if (add_extra_bin) {
|
||||||
if (periodic[i]) {
|
if (periodic[i]) {
|
||||||
// Shift the grid by half the bin width (values at edges instead of center of bins)
|
// Shift the grid by half the bin width (values at edges instead of center of bins)
|
||||||
lower_boundaries.push_back(cv[i]->lower_boundary.real_value - 0.5 * widths[i]);
|
lower_boundaries.push_back(cv[i]->lower_boundary.real_value - 0.5 * widths[i]);
|
||||||
@ -699,7 +701,7 @@ public:
|
|||||||
}
|
}
|
||||||
if (scale_factor != 1.0)
|
if (scale_factor != 1.0)
|
||||||
for (size_t i = 0; i < data.size(); i++) {
|
for (size_t i = 0; i < data.size(); i++) {
|
||||||
data[i] += scale_factor * other_grid.data[i];
|
data[i] += static_cast<T>(scale_factor * other_grid.data[i]);
|
||||||
}
|
}
|
||||||
else
|
else
|
||||||
// skip multiplication if possible
|
// skip multiplication if possible
|
||||||
@ -712,7 +714,7 @@ public:
|
|||||||
/// \brief Return the value suitable for output purposes (so that it
|
/// \brief Return the value suitable for output purposes (so that it
|
||||||
/// may be rescaled or manipulated without changing it permanently)
|
/// may be rescaled or manipulated without changing it permanently)
|
||||||
virtual inline T value_output(std::vector<int> const &ix,
|
virtual inline T value_output(std::vector<int> const &ix,
|
||||||
size_t const &imult = 0)
|
size_t const &imult = 0) const
|
||||||
{
|
{
|
||||||
return value(ix, imult);
|
return value(ix, imult);
|
||||||
}
|
}
|
||||||
@ -820,6 +822,8 @@ public:
|
|||||||
|
|
||||||
std::vector<int> old_nx = nx;
|
std::vector<int> old_nx = nx;
|
||||||
std::vector<colvarvalue> old_lb = lower_boundaries;
|
std::vector<colvarvalue> old_lb = lower_boundaries;
|
||||||
|
std::vector<colvarvalue> old_ub = upper_boundaries;
|
||||||
|
std::vector<cvm::real> old_w = widths;
|
||||||
|
|
||||||
{
|
{
|
||||||
size_t nd_in = 0;
|
size_t nd_in = 0;
|
||||||
@ -858,12 +862,15 @@ public:
|
|||||||
if (! periodic.size()) periodic.assign(nd, false);
|
if (! periodic.size()) periodic.assign(nd, false);
|
||||||
if (! widths.size()) widths.assign(nd, 1.0);
|
if (! widths.size()) widths.assign(nd, 1.0);
|
||||||
|
|
||||||
|
cvm::real eps = 1.e-10;
|
||||||
|
|
||||||
bool new_params = false;
|
bool new_params = false;
|
||||||
if (old_nx.size()) {
|
if (old_nx.size()) {
|
||||||
for (size_t i = 0; i < nd; i++) {
|
for (size_t i = 0; i < nd; i++) {
|
||||||
if ( (old_nx[i] != nx[i]) ||
|
if (old_nx[i] != nx[i] ||
|
||||||
(cvm::sqrt(cv[i]->dist2(old_lb[i],
|
cvm::sqrt(cv[i]->dist2(old_lb[i], lower_boundaries[i])) > eps ||
|
||||||
lower_boundaries[i])) > 1.0E-10) ) {
|
cvm::sqrt(cv[i]->dist2(old_ub[i], upper_boundaries[i])) > eps ||
|
||||||
|
cvm::fabs(old_w[i] - widths[i]) > eps) {
|
||||||
new_params = true;
|
new_params = true;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -928,7 +935,7 @@ public:
|
|||||||
/// \brief Read grid entry in restart file
|
/// \brief Read grid entry in restart file
|
||||||
std::istream & read_restart(std::istream &is)
|
std::istream & read_restart(std::istream &is)
|
||||||
{
|
{
|
||||||
size_t const start_pos = is.tellg();
|
std::streampos const start_pos = is.tellg();
|
||||||
std::string key, conf;
|
std::string key, conf;
|
||||||
if ((is >> key) && (key == std::string("grid_parameters"))) {
|
if ((is >> key) && (key == std::string("grid_parameters"))) {
|
||||||
is.seekg(start_pos, std::ios::beg);
|
is.seekg(start_pos, std::ios::beg);
|
||||||
@ -955,7 +962,7 @@ public:
|
|||||||
/// represented in memory
|
/// represented in memory
|
||||||
/// \param buf_size Number of values per line
|
/// \param buf_size Number of values per line
|
||||||
std::ostream & write_raw(std::ostream &os,
|
std::ostream & write_raw(std::ostream &os,
|
||||||
size_t const buf_size = 3)
|
size_t const buf_size = 3) const
|
||||||
{
|
{
|
||||||
std::streamsize const w = os.width();
|
std::streamsize const w = os.width();
|
||||||
std::streamsize const p = os.precision();
|
std::streamsize const p = os.precision();
|
||||||
@ -981,7 +988,7 @@ public:
|
|||||||
/// \brief Read data written by colvar_grid::write_raw()
|
/// \brief Read data written by colvar_grid::write_raw()
|
||||||
std::istream & read_raw(std::istream &is)
|
std::istream & read_raw(std::istream &is)
|
||||||
{
|
{
|
||||||
size_t const start_pos = is.tellg();
|
std::streampos const start_pos = is.tellg();
|
||||||
|
|
||||||
for (std::vector<int> ix = new_index(); index_ok(ix); incr(ix)) {
|
for (std::vector<int> ix = new_index(); index_ok(ix); incr(ix)) {
|
||||||
for (size_t imult = 0; imult < mult; imult++) {
|
for (size_t imult = 0; imult < mult; imult++) {
|
||||||
@ -1004,7 +1011,7 @@ public:
|
|||||||
|
|
||||||
/// \brief Write the grid in a format which is both human readable
|
/// \brief Write the grid in a format which is both human readable
|
||||||
/// and suitable for visualization e.g. with gnuplot
|
/// and suitable for visualization e.g. with gnuplot
|
||||||
void write_multicol(std::ostream &os)
|
void write_multicol(std::ostream &os) const
|
||||||
{
|
{
|
||||||
std::streamsize const w = os.width();
|
std::streamsize const w = os.width();
|
||||||
std::streamsize const p = os.precision();
|
std::streamsize const p = os.precision();
|
||||||
@ -1145,7 +1152,7 @@ public:
|
|||||||
|
|
||||||
/// \brief Write the grid data without labels, as they are
|
/// \brief Write the grid data without labels, as they are
|
||||||
/// represented in memory
|
/// represented in memory
|
||||||
std::ostream & write_opendx(std::ostream &os)
|
std::ostream & write_opendx(std::ostream &os) const
|
||||||
{
|
{
|
||||||
// write the header
|
// write the header
|
||||||
os << "object 1 class gridpositions counts";
|
os << "object 1 class gridpositions counts";
|
||||||
@ -1208,7 +1215,7 @@ public:
|
|||||||
/// Constructor from a vector of colvars
|
/// Constructor from a vector of colvars
|
||||||
colvar_grid_count(std::vector<colvar *> &colvars,
|
colvar_grid_count(std::vector<colvar *> &colvars,
|
||||||
size_t const &def_count = 0,
|
size_t const &def_count = 0,
|
||||||
bool margin = false);
|
bool add_extra_bin = false);
|
||||||
|
|
||||||
/// Increment the counter at given position
|
/// Increment the counter at given position
|
||||||
inline void incr_count(std::vector<int> const &ix)
|
inline void incr_count(std::vector<int> const &ix)
|
||||||
@ -1360,7 +1367,7 @@ public:
|
|||||||
|
|
||||||
/// Constructor from a vector of colvars
|
/// Constructor from a vector of colvars
|
||||||
colvar_grid_scalar(std::vector<colvar *> &colvars,
|
colvar_grid_scalar(std::vector<colvar *> &colvars,
|
||||||
bool margin = 0);
|
bool add_extra_bin = false);
|
||||||
|
|
||||||
/// Accumulate the value
|
/// Accumulate the value
|
||||||
inline void acc_value(std::vector<int> const &ix,
|
inline void acc_value(std::vector<int> const &ix,
|
||||||
@ -1419,9 +1426,9 @@ public:
|
|||||||
// 100 101 110 111 000 001 010 011
|
// 100 101 110 111 000 001 010 011
|
||||||
grad[0] = 0.25 * ((p[4] + p[5] + p[6] + p[7]) - (p[0] + p[1] + p[2] + p[3])) / widths[0];
|
grad[0] = 0.25 * ((p[4] + p[5] + p[6] + p[7]) - (p[0] + p[1] + p[2] + p[3])) / widths[0];
|
||||||
// 010 011 110 111 000 001 100 101
|
// 010 011 110 111 000 001 100 101
|
||||||
grad[1] = 0.25 * ((p[2] + p[3] + p[6] + p[7]) - (p[0] + p[1] + p[4] + p[5])) / widths[0];
|
grad[1] = 0.25 * ((p[2] + p[3] + p[6] + p[7]) - (p[0] + p[1] + p[4] + p[5])) / widths[1];
|
||||||
// 001 011 101 111 000 010 100 110
|
// 001 011 101 111 000 010 100 110
|
||||||
grad[2] = 0.25 * ((p[1] + p[3] + p[5] + p[7]) - (p[0] + p[2] + p[4] + p[6])) / widths[0];
|
grad[2] = 0.25 * ((p[1] + p[3] + p[5] + p[7]) - (p[0] + p[2] + p[4] + p[6])) / widths[2];
|
||||||
} else {
|
} else {
|
||||||
cvm::error("Finite differences available in dimension 2 and 3 only.");
|
cvm::error("Finite differences available in dimension 2 and 3 only.");
|
||||||
}
|
}
|
||||||
@ -1430,7 +1437,7 @@ public:
|
|||||||
/// \brief Return the value of the function at ix divided by its
|
/// \brief Return the value of the function at ix divided by its
|
||||||
/// number of samples (if the count grid is defined)
|
/// number of samples (if the count grid is defined)
|
||||||
virtual cvm::real value_output(std::vector<int> const &ix,
|
virtual cvm::real value_output(std::vector<int> const &ix,
|
||||||
size_t const &imult = 0)
|
size_t const &imult = 0) const
|
||||||
{
|
{
|
||||||
if (imult > 0) {
|
if (imult > 0) {
|
||||||
cvm::error("Error: trying to access a component "
|
cvm::error("Error: trying to access a component "
|
||||||
@ -1574,7 +1581,7 @@ public:
|
|||||||
/// \brief Return the value of the function at ix divided by its
|
/// \brief Return the value of the function at ix divided by its
|
||||||
/// number of samples (if the count grid is defined)
|
/// number of samples (if the count grid is defined)
|
||||||
virtual inline cvm::real value_output(std::vector<int> const &ix,
|
virtual inline cvm::real value_output(std::vector<int> const &ix,
|
||||||
size_t const &imult = 0)
|
size_t const &imult = 0) const
|
||||||
{
|
{
|
||||||
if (samples)
|
if (samples)
|
||||||
return (samples->value(ix) > 0) ?
|
return (samples->value(ix) > 0) ?
|
||||||
|
|||||||
@ -50,7 +50,7 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in)
|
|||||||
cvm::log("Initializing the collective variables module, version "+
|
cvm::log("Initializing the collective variables module, version "+
|
||||||
cvm::to_str(COLVARS_VERSION)+".\n");
|
cvm::to_str(COLVARS_VERSION)+".\n");
|
||||||
cvm::log("Please cite Fiorin et al, Mol Phys 2013:\n "
|
cvm::log("Please cite Fiorin et al, Mol Phys 2013:\n "
|
||||||
"https://doi.org/10.1080/00268976.2013.813594\n"
|
"https://dx.doi.org/10.1080/00268976.2013.813594\n"
|
||||||
"in any publication based on this calculation.\n");
|
"in any publication based on this calculation.\n");
|
||||||
|
|
||||||
if (proxy->smp_enabled() == COLVARS_OK) {
|
if (proxy->smp_enabled() == COLVARS_OK) {
|
||||||
@ -80,7 +80,7 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in)
|
|||||||
colvarmodule::rotation::crossing_threshold = 1.0e-02;
|
colvarmodule::rotation::crossing_threshold = 1.0e-02;
|
||||||
|
|
||||||
cv_traj_freq = 100;
|
cv_traj_freq = 100;
|
||||||
restart_out_freq = proxy->restart_frequency();
|
restart_out_freq = proxy->default_restart_frequency();
|
||||||
|
|
||||||
// by default overwrite the existing trajectory file
|
// by default overwrite the existing trajectory file
|
||||||
cv_traj_append = false;
|
cv_traj_append = false;
|
||||||
@ -91,7 +91,7 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in)
|
|||||||
|
|
||||||
colvarmodule * colvarmodule::main()
|
colvarmodule * colvarmodule::main()
|
||||||
{
|
{
|
||||||
return proxy->colvars;
|
return proxy ? proxy->colvars : NULL;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
@ -245,9 +245,6 @@ int colvarmodule::parse_config(std::string &conf)
|
|||||||
// Update any necessary proxy data
|
// Update any necessary proxy data
|
||||||
proxy->setup();
|
proxy->setup();
|
||||||
|
|
||||||
// configuration might have changed, better redo the labels
|
|
||||||
cv_traj_write_labels = true;
|
|
||||||
|
|
||||||
return get_error();
|
return get_error();
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -265,6 +262,12 @@ int colvarmodule::append_new_config(std::string const &new_conf)
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
void colvarmodule::config_changed()
|
||||||
|
{
|
||||||
|
cv_traj_write_labels = true;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
int colvarmodule::parse_global_params(std::string const &conf)
|
int colvarmodule::parse_global_params(std::string const &conf)
|
||||||
{
|
{
|
||||||
// TODO document and then echo this keyword
|
// TODO document and then echo this keyword
|
||||||
@ -332,8 +335,13 @@ int colvarmodule::parse_global_params(std::string const &conf)
|
|||||||
scripting_after_biases, scripting_after_biases);
|
scripting_after_biases, scripting_after_biases);
|
||||||
|
|
||||||
if (use_scripted_forces && !proxy->force_script_defined) {
|
if (use_scripted_forces && !proxy->force_script_defined) {
|
||||||
|
if (proxy->simulation_running()) {
|
||||||
return cvm::error("User script for scripted colvar forces not found.",
|
return cvm::error("User script for scripted colvar forces not found.",
|
||||||
INPUT_ERROR);
|
INPUT_ERROR);
|
||||||
|
} else {
|
||||||
|
// Not necessary if we are not applying biases in a real simulation (eg. VMD)
|
||||||
|
cvm::log("Warning: User script for scripted colvar forces not found.");
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
return cvm::get_error();
|
return cvm::get_error();
|
||||||
@ -369,6 +377,11 @@ int colvarmodule::parse_colvars(std::string const &conf)
|
|||||||
colvar_conf = "";
|
colvar_conf = "";
|
||||||
}
|
}
|
||||||
|
|
||||||
|
if (pos > 0) {
|
||||||
|
// One or more new variables were added
|
||||||
|
config_changed();
|
||||||
|
}
|
||||||
|
|
||||||
if (!colvars.size()) {
|
if (!colvars.size()) {
|
||||||
cvm::log("Warning: no collective variables defined.\n");
|
cvm::log("Warning: no collective variables defined.\n");
|
||||||
}
|
}
|
||||||
@ -419,6 +432,10 @@ int colvarmodule::parse_biases_type(std::string const &conf,
|
|||||||
}
|
}
|
||||||
bias_conf = "";
|
bias_conf = "";
|
||||||
}
|
}
|
||||||
|
if (conf_saved_pos > 0) {
|
||||||
|
// One or more new biases were added
|
||||||
|
config_changed();
|
||||||
|
}
|
||||||
return COLVARS_OK;
|
return COLVARS_OK;
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -656,6 +673,7 @@ std::string colvarmodule::read_colvar(std::string const &name)
|
|||||||
return ss.str();
|
return ss.str();
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
cvm::real colvarmodule::energy_difference(std::string const &bias_name,
|
cvm::real colvarmodule::energy_difference(std::string const &bias_name,
|
||||||
std::string const &conf)
|
std::string const &conf)
|
||||||
{
|
{
|
||||||
@ -672,75 +690,6 @@ cvm::real colvarmodule::energy_difference(std::string const &bias_name,
|
|||||||
return energy_diff;
|
return energy_diff;
|
||||||
}
|
}
|
||||||
|
|
||||||
int colvarmodule::bias_current_bin(std::string const &bias_name)
|
|
||||||
{
|
|
||||||
cvm::increase_depth();
|
|
||||||
int ret;
|
|
||||||
colvarbias *b = bias_by_name(bias_name);
|
|
||||||
|
|
||||||
if (b != NULL) {
|
|
||||||
ret = b->current_bin();
|
|
||||||
} else {
|
|
||||||
cvm::error("Error: bias not found.\n");
|
|
||||||
ret = COLVARS_ERROR;
|
|
||||||
}
|
|
||||||
|
|
||||||
cvm::decrease_depth();
|
|
||||||
return ret;
|
|
||||||
}
|
|
||||||
|
|
||||||
int colvarmodule::bias_bin_num(std::string const &bias_name)
|
|
||||||
{
|
|
||||||
cvm::increase_depth();
|
|
||||||
int ret;
|
|
||||||
colvarbias *b = bias_by_name(bias_name);
|
|
||||||
|
|
||||||
if (b != NULL) {
|
|
||||||
ret = b->bin_num();
|
|
||||||
} else {
|
|
||||||
cvm::error("Error: bias not found.\n");
|
|
||||||
ret = COLVARS_ERROR;
|
|
||||||
}
|
|
||||||
|
|
||||||
cvm::decrease_depth();
|
|
||||||
return ret;
|
|
||||||
}
|
|
||||||
|
|
||||||
int colvarmodule::bias_bin_count(std::string const &bias_name, size_t bin_index)
|
|
||||||
{
|
|
||||||
cvm::increase_depth();
|
|
||||||
int ret;
|
|
||||||
colvarbias *b = bias_by_name(bias_name);
|
|
||||||
|
|
||||||
if (b != NULL) {
|
|
||||||
ret = b->bin_count(bin_index);
|
|
||||||
} else {
|
|
||||||
cvm::error("Error: bias not found.\n");
|
|
||||||
ret = COLVARS_ERROR;
|
|
||||||
}
|
|
||||||
|
|
||||||
cvm::decrease_depth();
|
|
||||||
return ret;
|
|
||||||
}
|
|
||||||
|
|
||||||
int colvarmodule::bias_share(std::string const &bias_name)
|
|
||||||
{
|
|
||||||
cvm::increase_depth();
|
|
||||||
int ret;
|
|
||||||
colvarbias *b = bias_by_name(bias_name);
|
|
||||||
|
|
||||||
if (b != NULL) {
|
|
||||||
b->replica_share();
|
|
||||||
ret = COLVARS_OK;
|
|
||||||
} else {
|
|
||||||
cvm::error("Error: bias not found.\n");
|
|
||||||
ret = COLVARS_ERROR;
|
|
||||||
}
|
|
||||||
|
|
||||||
cvm::decrease_depth();
|
|
||||||
return ret;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
int colvarmodule::calc()
|
int colvarmodule::calc()
|
||||||
{
|
{
|
||||||
@ -753,11 +702,6 @@ int colvarmodule::calc()
|
|||||||
}
|
}
|
||||||
|
|
||||||
error_code |= calc_colvars();
|
error_code |= calc_colvars();
|
||||||
// set biasing forces to zero before biases are calculated and summed over
|
|
||||||
for (std::vector<colvar *>::iterator cvi = colvars.begin();
|
|
||||||
cvi != colvars.end(); cvi++) {
|
|
||||||
(*cvi)->reset_bias_force();
|
|
||||||
}
|
|
||||||
error_code |= calc_biases();
|
error_code |= calc_biases();
|
||||||
error_code |= update_colvar_forces();
|
error_code |= update_colvar_forces();
|
||||||
|
|
||||||
@ -768,17 +712,45 @@ int colvarmodule::calc()
|
|||||||
error_code |= write_traj_files();
|
error_code |= write_traj_files();
|
||||||
}
|
}
|
||||||
|
|
||||||
// write restart files, if needed
|
// write restart files and similar data
|
||||||
if (restart_out_freq && (cvm::step_relative() > 0) &&
|
if (restart_out_freq && (cvm::step_relative() > 0) &&
|
||||||
((cvm::step_absolute() % restart_out_freq) == 0) ) {
|
((cvm::step_absolute() % restart_out_freq) == 0) ) {
|
||||||
|
|
||||||
if (restart_out_name.size()) {
|
if (restart_out_name.size()) {
|
||||||
// Write restart file, if different from main output
|
// Write restart file, if different from main output
|
||||||
error_code |= write_restart_file(restart_out_name);
|
error_code |= write_restart_file(restart_out_name);
|
||||||
} else {
|
} else {
|
||||||
error_code |= write_restart_file(output_prefix()+".colvars.state");
|
error_code |= write_restart_file(output_prefix()+".colvars.state");
|
||||||
}
|
}
|
||||||
write_output_files();
|
|
||||||
|
cvm::increase_depth();
|
||||||
|
for (std::vector<colvar *>::iterator cvi = colvars.begin();
|
||||||
|
cvi != colvars.end();
|
||||||
|
cvi++) {
|
||||||
|
// TODO remove this when corrFunc becomes a bias
|
||||||
|
error_code |= (*cvi)->write_output_files();
|
||||||
}
|
}
|
||||||
|
for (std::vector<colvarbias *>::iterator bi = biases.begin();
|
||||||
|
bi != biases.end();
|
||||||
|
bi++) {
|
||||||
|
error_code |= (*bi)->write_state_to_replicas();
|
||||||
|
}
|
||||||
|
cvm::decrease_depth();
|
||||||
|
}
|
||||||
|
|
||||||
|
// Write output files for biases, at the specified frequency for each
|
||||||
|
cvm::increase_depth();
|
||||||
|
for (std::vector<colvarbias *>::iterator bi = biases.begin();
|
||||||
|
bi != biases.end();
|
||||||
|
bi++) {
|
||||||
|
if ((*bi)->output_freq > 0) {
|
||||||
|
if ((cvm::step_relative() > 0) &&
|
||||||
|
((cvm::step_absolute() % (*bi)->output_freq) == 0) ) {
|
||||||
|
error_code |= (*bi)->write_output_files();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
cvm::decrease_depth();
|
||||||
|
|
||||||
error_code |= end_of_step();
|
error_code |= end_of_step();
|
||||||
|
|
||||||
@ -885,6 +857,12 @@ int colvarmodule::calc_biases()
|
|||||||
if (cvm::debug() && num_biases())
|
if (cvm::debug() && num_biases())
|
||||||
cvm::log("Updating collective variable biases.\n");
|
cvm::log("Updating collective variable biases.\n");
|
||||||
|
|
||||||
|
// set biasing forces to zero before biases are calculated and summed over
|
||||||
|
for (std::vector<colvar *>::iterator cvi = colvars.begin();
|
||||||
|
cvi != colvars.end(); cvi++) {
|
||||||
|
(*cvi)->reset_bias_force();
|
||||||
|
}
|
||||||
|
|
||||||
std::vector<colvarbias *>::iterator bi;
|
std::vector<colvarbias *>::iterator bi;
|
||||||
int error_code = COLVARS_OK;
|
int error_code = COLVARS_OK;
|
||||||
|
|
||||||
@ -1031,12 +1009,32 @@ int colvarmodule::write_restart_file(std::string const &out_name)
|
|||||||
return cvm::error("Error: in writing restart file.\n", FILE_ERROR);
|
return cvm::error("Error: in writing restart file.\n", FILE_ERROR);
|
||||||
}
|
}
|
||||||
proxy->close_output_stream(out_name);
|
proxy->close_output_stream(out_name);
|
||||||
|
if (cv_traj_os != NULL) {
|
||||||
|
// Take the opportunity to flush colvars.traj
|
||||||
|
proxy->flush_output_stream(cv_traj_os);
|
||||||
|
}
|
||||||
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
|
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int colvarmodule::write_restart_string(std::string &output)
|
||||||
|
{
|
||||||
|
cvm::log("Saving state to output buffer.\n");
|
||||||
|
std::ostringstream os;
|
||||||
|
if (!write_restart(os)) {
|
||||||
|
return cvm::error("Error: in writing restart to buffer.\n", FILE_ERROR);
|
||||||
|
}
|
||||||
|
output = os.str();
|
||||||
|
return COLVARS_OK;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
int colvarmodule::write_traj_files()
|
int colvarmodule::write_traj_files()
|
||||||
{
|
{
|
||||||
|
if (cvm::debug()) {
|
||||||
|
cvm::log("colvarmodule::write_traj_files()\n");
|
||||||
|
}
|
||||||
|
|
||||||
if (cv_traj_os == NULL) {
|
if (cv_traj_os == NULL) {
|
||||||
if (open_traj_file(cv_traj_name) != COLVARS_OK) {
|
if (open_traj_file(cv_traj_name) != COLVARS_OK) {
|
||||||
return cvm::get_error();
|
return cvm::get_error();
|
||||||
@ -1057,15 +1055,12 @@ int colvarmodule::write_traj_files()
|
|||||||
write_traj(*cv_traj_os);
|
write_traj(*cv_traj_os);
|
||||||
}
|
}
|
||||||
|
|
||||||
if (restart_out_freq && (cv_traj_os != NULL)) {
|
if (restart_out_freq && (cv_traj_os != NULL) &&
|
||||||
// flush the trajectory file if we are at the restart frequency
|
((cvm::step_absolute() % restart_out_freq) == 0)) {
|
||||||
if ( (cvm::step_relative() > 0) &&
|
|
||||||
((cvm::step_absolute() % restart_out_freq) == 0) ) {
|
|
||||||
cvm::log("Synchronizing (emptying the buffer of) trajectory file \""+
|
cvm::log("Synchronizing (emptying the buffer of) trajectory file \""+
|
||||||
cv_traj_name+"\".\n");
|
cv_traj_name+"\".\n");
|
||||||
proxy->flush_output_stream(cv_traj_os);
|
proxy->flush_output_stream(cv_traj_os);
|
||||||
}
|
}
|
||||||
}
|
|
||||||
|
|
||||||
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
|
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
|
||||||
}
|
}
|
||||||
@ -1182,52 +1177,63 @@ int colvarmodule::reset()
|
|||||||
|
|
||||||
reset_index_groups();
|
reset_index_groups();
|
||||||
|
|
||||||
|
proxy->flush_output_streams();
|
||||||
proxy->reset();
|
proxy->reset();
|
||||||
|
|
||||||
if (cv_traj_os != NULL) {
|
|
||||||
// Do not close traj file here, as we might not be done with it yet.
|
|
||||||
proxy->flush_output_stream(cv_traj_os);
|
|
||||||
}
|
|
||||||
|
|
||||||
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
|
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
int colvarmodule::setup_input()
|
int colvarmodule::setup_input()
|
||||||
{
|
{
|
||||||
std::string restart_in_name("");
|
|
||||||
|
|
||||||
// read the restart configuration, if available
|
|
||||||
if (proxy->input_prefix().size()) {
|
if (proxy->input_prefix().size()) {
|
||||||
// read the restart file
|
// Read a state file
|
||||||
restart_in_name = proxy->input_prefix();
|
std::string restart_in_name(proxy->input_prefix()+
|
||||||
|
std::string(".colvars.state"));
|
||||||
std::ifstream input_is(restart_in_name.c_str());
|
std::ifstream input_is(restart_in_name.c_str());
|
||||||
if (!input_is.good()) {
|
if (!input_is.good()) {
|
||||||
// try by adding the suffix
|
// Try without the suffix
|
||||||
input_is.clear();
|
input_is.clear();
|
||||||
restart_in_name = restart_in_name+std::string(".colvars.state");
|
restart_in_name = proxy->input_prefix();
|
||||||
input_is.open(restart_in_name.c_str());
|
input_is.open(restart_in_name.c_str());
|
||||||
}
|
}
|
||||||
|
|
||||||
|
// Now that the file has been opened, clear this for the next round
|
||||||
|
proxy->input_prefix().clear();
|
||||||
|
|
||||||
if (!input_is.good()) {
|
if (!input_is.good()) {
|
||||||
cvm::error("Error: in opening input file \""+
|
return cvm::error("Error: in opening input state file \""+
|
||||||
std::string(restart_in_name)+"\".\n",
|
std::string(restart_in_name)+"\".\n",
|
||||||
FILE_ERROR);
|
FILE_ERROR);
|
||||||
return COLVARS_ERROR;
|
|
||||||
} else {
|
} else {
|
||||||
cvm::log(cvm::line_marker);
|
cvm::log(cvm::line_marker);
|
||||||
cvm::log("Restarting from file \""+restart_in_name+"\".\n");
|
cvm::log("Loading state from file \""+restart_in_name+"\".\n");
|
||||||
read_restart(input_is);
|
read_restart(input_is);
|
||||||
if (cvm::get_error() != COLVARS_OK) {
|
|
||||||
return COLVARS_ERROR;
|
|
||||||
} else {
|
|
||||||
proxy->input_prefix().clear();
|
|
||||||
}
|
|
||||||
cvm::log(cvm::line_marker);
|
cvm::log(cvm::line_marker);
|
||||||
|
return cvm::get_error();
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
if (proxy->input_buffer() != NULL) {
|
||||||
|
// Read a string buffer
|
||||||
|
char const *buffer = proxy->input_buffer();
|
||||||
|
size_t const buffer_size = strlen(proxy->input_buffer());
|
||||||
|
// Clear proxy pointer for the next round
|
||||||
|
proxy->input_buffer() = NULL;
|
||||||
|
if (buffer_size > 0) {
|
||||||
|
std::istringstream input_is;
|
||||||
|
// Replace the buffer of input_is; work around the lack of const in
|
||||||
|
// pubsetbuf's prototype (which also needs to support output streams)
|
||||||
|
input_is.rdbuf()->pubsetbuf(const_cast<char *>(buffer), buffer_size);
|
||||||
|
cvm::log(cvm::line_marker);
|
||||||
|
cvm::log("Loading state from input buffer.\n");
|
||||||
|
read_restart(input_is);
|
||||||
|
cvm::log(cvm::line_marker);
|
||||||
return cvm::get_error();
|
return cvm::get_error();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
return COLVARS_OK;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
@ -1277,6 +1283,20 @@ int colvarmodule::setup_output()
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
std::string colvarmodule::state_file_prefix(char const *filename)
|
||||||
|
{
|
||||||
|
std::string const filename_str(filename);
|
||||||
|
std::string const prefix =
|
||||||
|
filename_str.substr(0, filename_str.find(".colvars.state"));
|
||||||
|
if (prefix.size() == 0) {
|
||||||
|
cvm::error("Error: invalid filename/prefix value \""+filename_str+"\".",
|
||||||
|
INPUT_ERROR);
|
||||||
|
}
|
||||||
|
return prefix;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
std::istream & colvarmodule::read_restart(std::istream &is)
|
std::istream & colvarmodule::read_restart(std::istream &is)
|
||||||
{
|
{
|
||||||
bool warn_total_forces = false;
|
bool warn_total_forces = false;
|
||||||
@ -1340,7 +1360,7 @@ std::istream & colvarmodule::read_restart(std::istream &is)
|
|||||||
|
|
||||||
std::istream & colvarmodule::read_objects_state(std::istream &is)
|
std::istream & colvarmodule::read_objects_state(std::istream &is)
|
||||||
{
|
{
|
||||||
size_t pos = 0;
|
std::streampos pos = 0;
|
||||||
std::string word;
|
std::string word;
|
||||||
|
|
||||||
while (is.good()) {
|
while (is.good()) {
|
||||||
@ -1365,7 +1385,7 @@ std::istream & colvarmodule::read_objects_state(std::istream &is)
|
|||||||
"collective variable \""+(*cvi)->name+"\".\n",
|
"collective variable \""+(*cvi)->name+"\".\n",
|
||||||
INPUT_ERROR);
|
INPUT_ERROR);
|
||||||
}
|
}
|
||||||
if (static_cast<size_t>(is.tellg()) > pos) break; // found it
|
if (is.tellg() > pos) break; // found it
|
||||||
}
|
}
|
||||||
cvm::decrease_depth();
|
cvm::decrease_depth();
|
||||||
|
|
||||||
@ -1386,13 +1406,13 @@ std::istream & colvarmodule::read_objects_state(std::istream &is)
|
|||||||
(*bi)->name+"\".\n",
|
(*bi)->name+"\".\n",
|
||||||
INPUT_ERROR);
|
INPUT_ERROR);
|
||||||
}
|
}
|
||||||
if (static_cast<size_t>(is.tellg()) > pos) break; // found it
|
if (is.tellg() > pos) break; // found it
|
||||||
}
|
}
|
||||||
cvm::decrease_depth();
|
cvm::decrease_depth();
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
if (static_cast<size_t>(is.tellg()) == pos) {
|
if (is.tellg() == pos) {
|
||||||
// This block has not been read by any object: discard it and move on
|
// This block has not been read by any object: discard it and move on
|
||||||
// to the next one
|
// to the next one
|
||||||
is >> colvarparse::read_block(word, NULL);
|
is >> colvarparse::read_block(word, NULL);
|
||||||
@ -1438,34 +1458,21 @@ int colvarmodule::backup_file(char const *filename)
|
|||||||
int colvarmodule::write_output_files()
|
int colvarmodule::write_output_files()
|
||||||
{
|
{
|
||||||
int error_code = COLVARS_OK;
|
int error_code = COLVARS_OK;
|
||||||
|
|
||||||
cvm::increase_depth();
|
|
||||||
for (std::vector<colvar *>::iterator cvi = colvars.begin();
|
|
||||||
cvi != colvars.end();
|
|
||||||
cvi++) {
|
|
||||||
error_code |= (*cvi)->write_output_files();
|
|
||||||
}
|
|
||||||
cvm::decrease_depth();
|
|
||||||
|
|
||||||
cvm::increase_depth();
|
cvm::increase_depth();
|
||||||
for (std::vector<colvarbias *>::iterator bi = biases.begin();
|
for (std::vector<colvarbias *>::iterator bi = biases.begin();
|
||||||
bi != biases.end();
|
bi != biases.end();
|
||||||
bi++) {
|
bi++) {
|
||||||
|
// Only write output files if they have not already been written this time step
|
||||||
|
if ((*bi)->output_freq == 0 || (cvm::step_absolute() % (*bi)->output_freq) != 0) {
|
||||||
error_code |= (*bi)->write_output_files();
|
error_code |= (*bi)->write_output_files();
|
||||||
|
}
|
||||||
error_code |= (*bi)->write_state_to_replicas();
|
error_code |= (*bi)->write_state_to_replicas();
|
||||||
}
|
}
|
||||||
cvm::decrease_depth();
|
cvm::decrease_depth();
|
||||||
|
|
||||||
if (cv_traj_os != NULL) {
|
|
||||||
// do not close, there may be another run command
|
|
||||||
proxy->flush_output_stream(cv_traj_os);
|
|
||||||
}
|
|
||||||
|
|
||||||
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
|
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
int colvarmodule::read_traj(char const *traj_filename,
|
int colvarmodule::read_traj(char const *traj_filename,
|
||||||
long traj_read_begin,
|
long traj_read_begin,
|
||||||
long traj_read_end)
|
long traj_read_end)
|
||||||
@ -1581,12 +1588,10 @@ int colvarmodule::open_traj_file(std::string const &file_name)
|
|||||||
|
|
||||||
// (re)open trajectory file
|
// (re)open trajectory file
|
||||||
if (cv_traj_append) {
|
if (cv_traj_append) {
|
||||||
cvm::log("Appending to colvar trajectory file \""+file_name+
|
cvm::log("Appending to trajectory file \""+file_name+"\".\n");
|
||||||
"\".\n");
|
|
||||||
cv_traj_os = (cvm::proxy)->output_stream(file_name, std::ios::app);
|
cv_traj_os = (cvm::proxy)->output_stream(file_name, std::ios::app);
|
||||||
} else {
|
} else {
|
||||||
cvm::log("Writing to colvar trajectory file \""+file_name+
|
cvm::log("Opening trajectory file \""+file_name+"\".\n");
|
||||||
"\".\n");
|
|
||||||
proxy->backup_file(file_name.c_str());
|
proxy->backup_file(file_name.c_str());
|
||||||
cv_traj_os = (cvm::proxy)->output_stream(file_name);
|
cv_traj_os = (cvm::proxy)->output_stream(file_name);
|
||||||
}
|
}
|
||||||
@ -1603,6 +1608,7 @@ int colvarmodule::open_traj_file(std::string const &file_name)
|
|||||||
int colvarmodule::close_traj_file()
|
int colvarmodule::close_traj_file()
|
||||||
{
|
{
|
||||||
if (cv_traj_os != NULL) {
|
if (cv_traj_os != NULL) {
|
||||||
|
cvm::log("Closing trajectory file \""+cv_traj_name+"\".\n");
|
||||||
proxy->close_output_stream(cv_traj_name);
|
proxy->close_output_stream(cv_traj_name);
|
||||||
cv_traj_os = NULL;
|
cv_traj_os = NULL;
|
||||||
}
|
}
|
||||||
@ -1668,7 +1674,7 @@ std::ostream & colvarmodule::write_traj(std::ostream &os)
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
void cvm::log(std::string const &message, int min_log_level)
|
void colvarmodule::log(std::string const &message, int min_log_level)
|
||||||
{
|
{
|
||||||
if (cvm::log_level() < min_log_level) return;
|
if (cvm::log_level() < min_log_level) return;
|
||||||
// allow logging when the module is not fully initialized
|
// allow logging when the module is not fully initialized
|
||||||
@ -1681,13 +1687,13 @@ void cvm::log(std::string const &message, int min_log_level)
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
void cvm::increase_depth()
|
void colvarmodule::increase_depth()
|
||||||
{
|
{
|
||||||
(depth())++;
|
(depth())++;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
void cvm::decrease_depth()
|
void colvarmodule::decrease_depth()
|
||||||
{
|
{
|
||||||
if (depth() > 0) {
|
if (depth() > 0) {
|
||||||
(depth())--;
|
(depth())--;
|
||||||
@ -1695,7 +1701,7 @@ void cvm::decrease_depth()
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
size_t & cvm::depth()
|
size_t & colvarmodule::depth()
|
||||||
{
|
{
|
||||||
// NOTE: do not call log() or error() here, to avoid recursion
|
// NOTE: do not call log() or error() here, to avoid recursion
|
||||||
colvarmodule *cv = cvm::main();
|
colvarmodule *cv = cvm::main();
|
||||||
@ -1726,16 +1732,19 @@ void colvarmodule::set_error_bits(int code)
|
|||||||
proxy->smp_unlock();
|
proxy->smp_unlock();
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
bool colvarmodule::get_error_bit(int code)
|
bool colvarmodule::get_error_bit(int code)
|
||||||
{
|
{
|
||||||
return bool(errorCode & code);
|
return bool(errorCode & code);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
void colvarmodule::clear_error()
|
void colvarmodule::clear_error()
|
||||||
{
|
{
|
||||||
proxy->smp_lock();
|
proxy->smp_lock();
|
||||||
errorCode = COLVARS_OK;
|
errorCode = COLVARS_OK;
|
||||||
proxy->smp_unlock();
|
proxy->smp_unlock();
|
||||||
|
proxy->clear_error_msgs();
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
@ -1749,9 +1758,7 @@ int colvarmodule::error(std::string const &message, int code)
|
|||||||
|
|
||||||
int colvarmodule::fatal_error(std::string const &message)
|
int colvarmodule::fatal_error(std::string const &message)
|
||||||
{
|
{
|
||||||
set_error_bits(FATAL_ERROR);
|
return error(message, FATAL_ERROR);
|
||||||
proxy->fatal_error(message);
|
|
||||||
return get_error();
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
@ -1793,7 +1800,7 @@ int cvm::read_index_file(char const *filename)
|
|||||||
std::vector<int> *new_index_group = new std::vector<int>();
|
std::vector<int> *new_index_group = new std::vector<int>();
|
||||||
|
|
||||||
int atom_number = 1;
|
int atom_number = 1;
|
||||||
size_t pos = is.tellg();
|
std::streampos pos = is.tellg();
|
||||||
while ( (is >> atom_number) && (atom_number > 0) ) {
|
while ( (is >> atom_number) && (atom_number > 0) ) {
|
||||||
new_index_group->push_back(atom_number);
|
new_index_group->push_back(atom_number);
|
||||||
pos = is.tellg();
|
pos = is.tellg();
|
||||||
|
|||||||
@ -221,7 +221,6 @@ public:
|
|||||||
|
|
||||||
static void clear_error();
|
static void clear_error();
|
||||||
|
|
||||||
|
|
||||||
/// Current step number
|
/// Current step number
|
||||||
static step_number it;
|
static step_number it;
|
||||||
/// Starting step number for this run
|
/// Starting step number for this run
|
||||||
@ -371,6 +370,9 @@ public:
|
|||||||
/// anything that triggers another call
|
/// anything that triggers another call
|
||||||
int append_new_config(std::string const &conf);
|
int append_new_config(std::string const &conf);
|
||||||
|
|
||||||
|
/// Signals to the module object that the configuration has changed
|
||||||
|
void config_changed();
|
||||||
|
|
||||||
private:
|
private:
|
||||||
|
|
||||||
/// Configuration string read so far by the module (includes comments)
|
/// Configuration string read so far by the module (includes comments)
|
||||||
@ -441,6 +443,9 @@ public:
|
|||||||
/// Write the output restart file
|
/// Write the output restart file
|
||||||
std::ostream & write_restart(std::ostream &os);
|
std::ostream & write_restart(std::ostream &os);
|
||||||
|
|
||||||
|
/// Strips .colvars.state from filename and checks that it is not empty
|
||||||
|
static std::string state_file_prefix(char const *filename);
|
||||||
|
|
||||||
/// Open a trajectory file if requested (and leave it open)
|
/// Open a trajectory file if requested (and leave it open)
|
||||||
int open_traj_file(std::string const &file_name);
|
int open_traj_file(std::string const &file_name);
|
||||||
/// Close it (note: currently unused)
|
/// Close it (note: currently unused)
|
||||||
@ -459,6 +464,9 @@ public:
|
|||||||
/// Backup a file before writing it
|
/// Backup a file before writing it
|
||||||
static int backup_file(char const *filename);
|
static int backup_file(char const *filename);
|
||||||
|
|
||||||
|
/// Write the state into a string
|
||||||
|
int write_restart_string(std::string &output);
|
||||||
|
|
||||||
/// Look up a bias by name; returns NULL if not found
|
/// Look up a bias by name; returns NULL if not found
|
||||||
static colvarbias * bias_by_name(std::string const &name);
|
static colvarbias * bias_by_name(std::string const &name);
|
||||||
|
|
||||||
@ -479,15 +487,6 @@ public:
|
|||||||
/// currently works for harmonic (force constant and/or centers)
|
/// currently works for harmonic (force constant and/or centers)
|
||||||
real energy_difference(std::string const &bias_name, std::string const &conf);
|
real energy_difference(std::string const &bias_name, std::string const &conf);
|
||||||
|
|
||||||
/// Give the total number of bins for a given bias.
|
|
||||||
int bias_bin_num(std::string const &bias_name);
|
|
||||||
/// Calculate the bin index for a given bias.
|
|
||||||
int bias_current_bin(std::string const &bias_name);
|
|
||||||
//// Give the count at a given bin index.
|
|
||||||
int bias_bin_count(std::string const &bias_name, size_t bin_index);
|
|
||||||
//// Share among replicas.
|
|
||||||
int bias_share(std::string const &bias_name);
|
|
||||||
|
|
||||||
/// Main worker function
|
/// Main worker function
|
||||||
int calc();
|
int calc();
|
||||||
|
|
||||||
|
|||||||
@ -853,7 +853,7 @@ colvarparse::read_block::~read_block()
|
|||||||
|
|
||||||
std::istream & operator>> (std::istream &is, colvarparse::read_block const &rb)
|
std::istream & operator>> (std::istream &is, colvarparse::read_block const &rb)
|
||||||
{
|
{
|
||||||
size_t start_pos = is.tellg();
|
std::streampos start_pos = is.tellg();
|
||||||
std::string read_key, next;
|
std::string read_key, next;
|
||||||
|
|
||||||
if ( !(is >> read_key) || !(read_key == rb.key) ||
|
if ( !(is >> read_key) || !(read_key == rb.key) ||
|
||||||
|
|||||||
@ -20,11 +20,6 @@
|
|||||||
#include <omp.h>
|
#include <omp.h>
|
||||||
#endif
|
#endif
|
||||||
|
|
||||||
#if defined(NAMD_TCL) || defined(VMDTCL)
|
|
||||||
#define COLVARS_TCL
|
|
||||||
#include <tcl.h>
|
|
||||||
#endif
|
|
||||||
|
|
||||||
#include "colvarmodule.h"
|
#include "colvarmodule.h"
|
||||||
#include "colvarproxy.h"
|
#include "colvarproxy.h"
|
||||||
#include "colvarscript.h"
|
#include "colvarscript.h"
|
||||||
@ -33,8 +28,9 @@
|
|||||||
|
|
||||||
|
|
||||||
colvarproxy_system::colvarproxy_system()
|
colvarproxy_system::colvarproxy_system()
|
||||||
: angstrom_value(0.)
|
|
||||||
{
|
{
|
||||||
|
angstrom_value = 0.0;
|
||||||
|
total_force_requested = false;
|
||||||
reset_pbc_lattice();
|
reset_pbc_lattice();
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -67,7 +63,7 @@ bool colvarproxy_system::total_forces_same_step() const
|
|||||||
|
|
||||||
inline int round_to_integer(cvm::real x)
|
inline int round_to_integer(cvm::real x)
|
||||||
{
|
{
|
||||||
return cvm::floor(x+0.5);
|
return int(cvm::floor(x+0.5));
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
@ -135,6 +131,14 @@ cvm::rvector colvarproxy_system::position_distance(cvm::atom_pos const &pos1,
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int colvarproxy_system::get_molid(int &)
|
||||||
|
{
|
||||||
|
cvm::error("Error: only VMD allows the use of multiple \"molecules\", "
|
||||||
|
"i.e. multiple molecular systems.", COLVARS_NOT_IMPLEMENTED);
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
colvarproxy_atoms::colvarproxy_atoms()
|
colvarproxy_atoms::colvarproxy_atoms()
|
||||||
{
|
{
|
||||||
@ -505,144 +509,12 @@ int colvarproxy_script::run_colvar_gradient_callback(std::string const & /* name
|
|||||||
|
|
||||||
|
|
||||||
|
|
||||||
colvarproxy_tcl::colvarproxy_tcl()
|
colvarproxy_io::colvarproxy_io()
|
||||||
{
|
{
|
||||||
tcl_interp_ = NULL;
|
input_buffer_ = NULL;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
colvarproxy_tcl::~colvarproxy_tcl()
|
|
||||||
{
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
void colvarproxy_tcl::init_tcl_pointers()
|
|
||||||
{
|
|
||||||
cvm::error("Error: Tcl support is currently unavailable "
|
|
||||||
"outside NAMD or VMD.\n", COLVARS_NOT_IMPLEMENTED);
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
char const *colvarproxy_tcl::tcl_obj_to_str(unsigned char *obj)
|
|
||||||
{
|
|
||||||
#if defined(COLVARS_TCL)
|
|
||||||
return Tcl_GetString(reinterpret_cast<Tcl_Obj *>(obj));
|
|
||||||
#else
|
|
||||||
return NULL;
|
|
||||||
#endif
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
int colvarproxy_tcl::tcl_run_force_callback()
|
|
||||||
{
|
|
||||||
#if defined(COLVARS_TCL)
|
|
||||||
Tcl_Interp *const tcl_interp = reinterpret_cast<Tcl_Interp *>(tcl_interp_);
|
|
||||||
std::string cmd = std::string("calc_colvar_forces ")
|
|
||||||
+ cvm::to_str(cvm::step_absolute());
|
|
||||||
int err = Tcl_Eval(tcl_interp, cmd.c_str());
|
|
||||||
if (err != TCL_OK) {
|
|
||||||
cvm::log(std::string("Error while executing calc_colvar_forces:\n"));
|
|
||||||
cvm::error(Tcl_GetStringResult(tcl_interp));
|
|
||||||
return COLVARS_ERROR;
|
|
||||||
}
|
|
||||||
return cvm::get_error();
|
|
||||||
#else
|
|
||||||
return COLVARS_NOT_IMPLEMENTED;
|
|
||||||
#endif
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
int colvarproxy_tcl::tcl_run_colvar_callback(
|
|
||||||
std::string const & name,
|
|
||||||
std::vector<const colvarvalue *> const & cvc_values,
|
|
||||||
colvarvalue & value)
|
|
||||||
{
|
|
||||||
#if defined(COLVARS_TCL)
|
|
||||||
|
|
||||||
Tcl_Interp *const tcl_interp = reinterpret_cast<Tcl_Interp *>(tcl_interp_);
|
|
||||||
size_t i;
|
|
||||||
std::string cmd = std::string("calc_") + name;
|
|
||||||
for (i = 0; i < cvc_values.size(); i++) {
|
|
||||||
cmd += std::string(" {") + (*(cvc_values[i])).to_simple_string() +
|
|
||||||
std::string("}");
|
|
||||||
}
|
|
||||||
int err = Tcl_Eval(tcl_interp, cmd.c_str());
|
|
||||||
const char *result = Tcl_GetStringResult(tcl_interp);
|
|
||||||
if (err != TCL_OK) {
|
|
||||||
return cvm::error(std::string("Error while executing ")
|
|
||||||
+ cmd + std::string(":\n") +
|
|
||||||
std::string(Tcl_GetStringResult(tcl_interp)), COLVARS_ERROR);
|
|
||||||
}
|
|
||||||
std::istringstream is(result);
|
|
||||||
if (value.from_simple_string(is.str()) != COLVARS_OK) {
|
|
||||||
cvm::log("Error parsing colvar value from script:");
|
|
||||||
cvm::error(result);
|
|
||||||
return COLVARS_ERROR;
|
|
||||||
}
|
|
||||||
return cvm::get_error();
|
|
||||||
|
|
||||||
#else
|
|
||||||
|
|
||||||
return COLVARS_NOT_IMPLEMENTED;
|
|
||||||
|
|
||||||
#endif
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
int colvarproxy_tcl::tcl_run_colvar_gradient_callback(
|
|
||||||
std::string const & name,
|
|
||||||
std::vector<const colvarvalue *> const & cvc_values,
|
|
||||||
std::vector<cvm::matrix2d<cvm::real> > & gradient)
|
|
||||||
{
|
|
||||||
#if defined(COLVARS_TCL)
|
|
||||||
|
|
||||||
Tcl_Interp *const tcl_interp = reinterpret_cast<Tcl_Interp *>(tcl_interp_);
|
|
||||||
size_t i;
|
|
||||||
std::string cmd = std::string("calc_") + name + "_gradient";
|
|
||||||
for (i = 0; i < cvc_values.size(); i++) {
|
|
||||||
cmd += std::string(" {") + (*(cvc_values[i])).to_simple_string() +
|
|
||||||
std::string("}");
|
|
||||||
}
|
|
||||||
int err = Tcl_Eval(tcl_interp, cmd.c_str());
|
|
||||||
if (err != TCL_OK) {
|
|
||||||
return cvm::error(std::string("Error while executing ")
|
|
||||||
+ cmd + std::string(":\n") +
|
|
||||||
std::string(Tcl_GetStringResult(tcl_interp)), COLVARS_ERROR);
|
|
||||||
}
|
|
||||||
Tcl_Obj **list;
|
|
||||||
int n;
|
|
||||||
Tcl_ListObjGetElements(tcl_interp, Tcl_GetObjResult(tcl_interp),
|
|
||||||
&n, &list);
|
|
||||||
if (n != int(gradient.size())) {
|
|
||||||
cvm::error("Error parsing list of gradient values from script: found "
|
|
||||||
+ cvm::to_str(n) + " values instead of " +
|
|
||||||
cvm::to_str(gradient.size()));
|
|
||||||
return COLVARS_ERROR;
|
|
||||||
}
|
|
||||||
for (i = 0; i < gradient.size(); i++) {
|
|
||||||
std::istringstream is(Tcl_GetString(list[i]));
|
|
||||||
if (gradient[i].from_simple_string(is.str()) != COLVARS_OK) {
|
|
||||||
cvm::log("Gradient matrix size: " + cvm::to_str(gradient[i].size()));
|
|
||||||
cvm::log("Gradient string: " + cvm::to_str(Tcl_GetString(list[i])));
|
|
||||||
cvm::error("Error parsing gradient value from script", COLVARS_ERROR);
|
|
||||||
return COLVARS_ERROR;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
return cvm::get_error();
|
|
||||||
|
|
||||||
#else
|
|
||||||
|
|
||||||
return COLVARS_NOT_IMPLEMENTED;
|
|
||||||
|
|
||||||
#endif
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
colvarproxy_io::colvarproxy_io() {}
|
|
||||||
|
|
||||||
|
|
||||||
colvarproxy_io::~colvarproxy_io() {}
|
colvarproxy_io::~colvarproxy_io() {}
|
||||||
|
|
||||||
|
|
||||||
@ -658,78 +530,6 @@ int colvarproxy_io::set_frame(long int)
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
std::ostream * colvarproxy_io::output_stream(std::string const &output_name,
|
|
||||||
std::ios_base::openmode mode)
|
|
||||||
{
|
|
||||||
if (cvm::debug()) {
|
|
||||||
cvm::log("Using colvarproxy::output_stream()\n");
|
|
||||||
}
|
|
||||||
|
|
||||||
std::ostream *os = get_output_stream(output_name);
|
|
||||||
if (os != NULL) return os;
|
|
||||||
|
|
||||||
if (!(mode & (std::ios_base::app | std::ios_base::ate))) {
|
|
||||||
backup_file(output_name);
|
|
||||||
}
|
|
||||||
std::ofstream *osf = new std::ofstream(output_name.c_str(), mode);
|
|
||||||
if (!osf->is_open()) {
|
|
||||||
cvm::error("Error: cannot write to file/channel \""+output_name+"\".\n",
|
|
||||||
FILE_ERROR);
|
|
||||||
return NULL;
|
|
||||||
}
|
|
||||||
output_stream_names.push_back(output_name);
|
|
||||||
output_files.push_back(osf);
|
|
||||||
return osf;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
std::ostream *colvarproxy_io::get_output_stream(std::string const &output_name)
|
|
||||||
{
|
|
||||||
std::list<std::ostream *>::iterator osi = output_files.begin();
|
|
||||||
std::list<std::string>::iterator osni = output_stream_names.begin();
|
|
||||||
for ( ; osi != output_files.end(); osi++, osni++) {
|
|
||||||
if (*osni == output_name) {
|
|
||||||
return *osi;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
return NULL;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
int colvarproxy_io::flush_output_stream(std::ostream *os)
|
|
||||||
{
|
|
||||||
std::list<std::ostream *>::iterator osi = output_files.begin();
|
|
||||||
std::list<std::string>::iterator osni = output_stream_names.begin();
|
|
||||||
for ( ; osi != output_files.end(); osi++, osni++) {
|
|
||||||
if (*osi == os) {
|
|
||||||
((std::ofstream *) (*osi))->flush();
|
|
||||||
return COLVARS_OK;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
return cvm::error("Error: trying to flush an output file/channel "
|
|
||||||
"that wasn't open.\n", BUG_ERROR);
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
int colvarproxy_io::close_output_stream(std::string const &output_name)
|
|
||||||
{
|
|
||||||
std::list<std::ostream *>::iterator osi = output_files.begin();
|
|
||||||
std::list<std::string>::iterator osni = output_stream_names.begin();
|
|
||||||
for ( ; osi != output_files.end(); osi++, osni++) {
|
|
||||||
if (*osni == output_name) {
|
|
||||||
((std::ofstream *) (*osi))->close();
|
|
||||||
delete *osi;
|
|
||||||
output_files.erase(osi);
|
|
||||||
output_stream_names.erase(osni);
|
|
||||||
return COLVARS_OK;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
return cvm::error("Error: trying to close an output file/channel "
|
|
||||||
"that wasn't open.\n", BUG_ERROR);
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
int colvarproxy_io::backup_file(char const * /* filename */)
|
int colvarproxy_io::backup_file(char const * /* filename */)
|
||||||
{
|
{
|
||||||
// TODO implement this using rename_file()
|
// TODO implement this using rename_file()
|
||||||
@ -796,11 +596,33 @@ colvarproxy::colvarproxy()
|
|||||||
{
|
{
|
||||||
colvars = NULL;
|
colvars = NULL;
|
||||||
b_simulation_running = true;
|
b_simulation_running = true;
|
||||||
|
b_simulation_continuing = false;
|
||||||
b_delete_requested = false;
|
b_delete_requested = false;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
colvarproxy::~colvarproxy() {}
|
colvarproxy::~colvarproxy()
|
||||||
|
{
|
||||||
|
close_files();
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int colvarproxy::close_files()
|
||||||
|
{
|
||||||
|
if (smp_enabled() == COLVARS_OK && smp_thread_id() > 0) {
|
||||||
|
// Nothing to do on non-master threads
|
||||||
|
return COLVARS_OK;
|
||||||
|
}
|
||||||
|
std::list<std::string>::iterator osni = output_stream_names.begin();
|
||||||
|
std::list<std::ostream *>::iterator osi = output_files.begin();
|
||||||
|
for ( ; osi != output_files.end(); osi++, osni++) {
|
||||||
|
((std::ofstream *) (*osi))->close();
|
||||||
|
delete *osi;
|
||||||
|
}
|
||||||
|
output_files.clear();
|
||||||
|
output_stream_names.clear();
|
||||||
|
return COLVARS_OK;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
int colvarproxy::reset()
|
int colvarproxy::reset()
|
||||||
@ -838,9 +660,37 @@ int colvarproxy::update_output()
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
size_t colvarproxy::restart_frequency()
|
int colvarproxy::post_run()
|
||||||
{
|
{
|
||||||
return 0;
|
int error_code = COLVARS_OK;
|
||||||
|
if (colvars->output_prefix().size()) {
|
||||||
|
error_code |= colvars->write_restart_file(cvm::output_prefix()+".colvars.state");
|
||||||
|
error_code |= colvars->write_output_files();
|
||||||
|
}
|
||||||
|
error_code |= flush_output_streams();
|
||||||
|
return error_code;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
void colvarproxy::add_error_msg(std::string const &message)
|
||||||
|
{
|
||||||
|
std::istringstream is(message);
|
||||||
|
std::string line;
|
||||||
|
while (std::getline(is, line)) {
|
||||||
|
error_output += line+"\n";
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
void colvarproxy::clear_error_msgs()
|
||||||
|
{
|
||||||
|
error_output.clear();
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
std::string const & colvarproxy::get_error_msgs()
|
||||||
|
{
|
||||||
|
return error_output;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
@ -852,3 +702,105 @@ int colvarproxy::get_version_from_string(char const *version_string)
|
|||||||
is >> newint;
|
is >> newint;
|
||||||
return newint;
|
return newint;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
void colvarproxy::smp_stream_error()
|
||||||
|
{
|
||||||
|
cvm::error("Error: trying to access an output stream from a "
|
||||||
|
"multi-threaded region (bug). For a quick workaround, use "
|
||||||
|
"\"smp off\" in the Colvars config.\n", BUG_ERROR);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
std::ostream * colvarproxy::output_stream(std::string const &output_name,
|
||||||
|
std::ios_base::openmode mode)
|
||||||
|
{
|
||||||
|
if (cvm::debug()) {
|
||||||
|
cvm::log("Using colvarproxy::output_stream()\n");
|
||||||
|
}
|
||||||
|
|
||||||
|
std::ostream *os = get_output_stream(output_name);
|
||||||
|
if (os != NULL) return os;
|
||||||
|
|
||||||
|
if (!(mode & (std::ios_base::app | std::ios_base::ate))) {
|
||||||
|
backup_file(output_name);
|
||||||
|
}
|
||||||
|
std::ofstream *osf = new std::ofstream(output_name.c_str(), mode);
|
||||||
|
if (!osf->is_open()) {
|
||||||
|
cvm::error("Error: cannot write to file/channel \""+output_name+"\".\n",
|
||||||
|
FILE_ERROR);
|
||||||
|
return NULL;
|
||||||
|
}
|
||||||
|
output_stream_names.push_back(output_name);
|
||||||
|
output_files.push_back(osf);
|
||||||
|
return osf;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
std::ostream *colvarproxy::get_output_stream(std::string const &output_name)
|
||||||
|
{
|
||||||
|
if (smp_enabled() == COLVARS_OK) {
|
||||||
|
if (smp_thread_id() > 0) smp_stream_error();
|
||||||
|
}
|
||||||
|
std::list<std::ostream *>::iterator osi = output_files.begin();
|
||||||
|
std::list<std::string>::iterator osni = output_stream_names.begin();
|
||||||
|
for ( ; osi != output_files.end(); osi++, osni++) {
|
||||||
|
if (*osni == output_name) {
|
||||||
|
return *osi;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return NULL;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
int colvarproxy::flush_output_stream(std::ostream *os)
|
||||||
|
{
|
||||||
|
if (smp_enabled() == COLVARS_OK) {
|
||||||
|
if (smp_thread_id() > 0) smp_stream_error();
|
||||||
|
}
|
||||||
|
std::list<std::ostream *>::iterator osi = output_files.begin();
|
||||||
|
std::list<std::string>::iterator osni = output_stream_names.begin();
|
||||||
|
for ( ; osi != output_files.end(); osi++, osni++) {
|
||||||
|
if (*osi == os) {
|
||||||
|
((std::ofstream *) (*osi))->flush();
|
||||||
|
return COLVARS_OK;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return cvm::error("Error: trying to flush an output file/channel "
|
||||||
|
"that wasn't open.\n", BUG_ERROR);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int colvarproxy::flush_output_streams()
|
||||||
|
{
|
||||||
|
if (smp_enabled() == COLVARS_OK && smp_thread_id() > 0)
|
||||||
|
return COLVARS_OK;
|
||||||
|
|
||||||
|
std::list<std::ostream *>::iterator osi = output_files.begin();
|
||||||
|
for ( ; osi != output_files.end(); osi++) {
|
||||||
|
((std::ofstream *) (*osi))->flush();
|
||||||
|
}
|
||||||
|
return COLVARS_OK;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int colvarproxy::close_output_stream(std::string const &output_name)
|
||||||
|
{
|
||||||
|
if (smp_enabled() == COLVARS_OK) {
|
||||||
|
if (smp_thread_id() > 0) smp_stream_error();
|
||||||
|
}
|
||||||
|
std::list<std::ostream *>::iterator osi = output_files.begin();
|
||||||
|
std::list<std::string>::iterator osni = output_stream_names.begin();
|
||||||
|
for ( ; osi != output_files.end(); osi++, osni++) {
|
||||||
|
if (*osni == output_name) {
|
||||||
|
((std::ofstream *) (*osi))->close();
|
||||||
|
delete *osi;
|
||||||
|
output_files.erase(osi);
|
||||||
|
output_stream_names.erase(osni);
|
||||||
|
return COLVARS_OK;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return cvm::error("Error: trying to close an output file/channel "
|
||||||
|
"that wasn't open.\n", BUG_ERROR);
|
||||||
|
}
|
||||||
|
|||||||
@ -16,7 +16,8 @@
|
|||||||
#include "colvarmodule.h"
|
#include "colvarmodule.h"
|
||||||
#include "colvartypes.h"
|
#include "colvartypes.h"
|
||||||
#include "colvarvalue.h"
|
#include "colvarvalue.h"
|
||||||
|
#include "colvarproxy_tcl.h"
|
||||||
|
#include "colvarproxy_volmaps.h"
|
||||||
|
|
||||||
/// \file colvarproxy.h
|
/// \file colvarproxy.h
|
||||||
/// \brief Colvars proxy classes
|
/// \brief Colvars proxy classes
|
||||||
@ -29,7 +30,7 @@
|
|||||||
///
|
///
|
||||||
/// To interface to a new MD engine, the simplest solution is to derive a new
|
/// To interface to a new MD engine, the simplest solution is to derive a new
|
||||||
/// class from \link colvarproxy \endlink. Currently implemented are: \link
|
/// class from \link colvarproxy \endlink. Currently implemented are: \link
|
||||||
/// colvarproxy_lammps \endlink, \link colvarproxy_namd \endlink, \link
|
/// colvarproxy_lammps, \endlink, \link colvarproxy_namd, \endlink, \link
|
||||||
/// colvarproxy_vmd \endlink.
|
/// colvarproxy_vmd \endlink.
|
||||||
|
|
||||||
|
|
||||||
@ -121,8 +122,15 @@ public:
|
|||||||
/// Are total forces from the current step available?
|
/// Are total forces from the current step available?
|
||||||
virtual bool total_forces_same_step() const;
|
virtual bool total_forces_same_step() const;
|
||||||
|
|
||||||
|
/// Get the molecule ID when called in VMD; raise error otherwise
|
||||||
|
/// \param molid Set this argument equal to the current VMD molid
|
||||||
|
virtual int get_molid(int &molid);
|
||||||
|
|
||||||
protected:
|
protected:
|
||||||
|
|
||||||
|
/// Whether the total forces have been requested
|
||||||
|
bool total_force_requested;
|
||||||
|
|
||||||
/// \brief Type of boundary conditions
|
/// \brief Type of boundary conditions
|
||||||
///
|
///
|
||||||
/// Orthogonal and triclinic cells are made available to objects.
|
/// Orthogonal and triclinic cells are made available to objects.
|
||||||
@ -542,46 +550,6 @@ public:
|
|||||||
};
|
};
|
||||||
|
|
||||||
|
|
||||||
/// Methods for using Tcl within Colvars
|
|
||||||
class colvarproxy_tcl {
|
|
||||||
|
|
||||||
public:
|
|
||||||
|
|
||||||
/// Constructor
|
|
||||||
colvarproxy_tcl();
|
|
||||||
|
|
||||||
/// Destructor
|
|
||||||
virtual ~colvarproxy_tcl();
|
|
||||||
|
|
||||||
/// Is Tcl available? (trigger initialization if needed)
|
|
||||||
int tcl_available();
|
|
||||||
|
|
||||||
/// Tcl implementation of script_obj_to_str()
|
|
||||||
char const *tcl_obj_to_str(unsigned char *obj);
|
|
||||||
|
|
||||||
/// Run a user-defined colvar forces script
|
|
||||||
int tcl_run_force_callback();
|
|
||||||
|
|
||||||
int tcl_run_colvar_callback(
|
|
||||||
std::string const &name,
|
|
||||||
std::vector<const colvarvalue *> const &cvcs,
|
|
||||||
colvarvalue &value);
|
|
||||||
|
|
||||||
int tcl_run_colvar_gradient_callback(
|
|
||||||
std::string const &name,
|
|
||||||
std::vector<const colvarvalue *> const &cvcs,
|
|
||||||
std::vector<cvm::matrix2d<cvm::real> > &gradient);
|
|
||||||
|
|
||||||
protected:
|
|
||||||
|
|
||||||
/// Pointer to Tcl interpreter object
|
|
||||||
void *tcl_interp_;
|
|
||||||
|
|
||||||
/// Set Tcl pointers
|
|
||||||
virtual void init_tcl_pointers();
|
|
||||||
};
|
|
||||||
|
|
||||||
|
|
||||||
/// Methods for data input/output
|
/// Methods for data input/output
|
||||||
class colvarproxy_io {
|
class colvarproxy_io {
|
||||||
|
|
||||||
@ -601,21 +569,6 @@ public:
|
|||||||
// Returns error code
|
// Returns error code
|
||||||
virtual int set_frame(long int);
|
virtual int set_frame(long int);
|
||||||
|
|
||||||
/// \brief Returns a reference to the given output channel;
|
|
||||||
/// if this is not open already, then open it
|
|
||||||
virtual std::ostream *output_stream(std::string const &output_name,
|
|
||||||
std::ios_base::openmode mode =
|
|
||||||
std::ios_base::out);
|
|
||||||
|
|
||||||
/// Returns a reference to output_name if it exists, NULL otherwise
|
|
||||||
virtual std::ostream *get_output_stream(std::string const &output_name);
|
|
||||||
|
|
||||||
/// \brief Flushes the given output channel
|
|
||||||
virtual int flush_output_stream(std::ostream *os);
|
|
||||||
|
|
||||||
/// \brief Closes the given output channel
|
|
||||||
virtual int close_output_stream(std::string const &output_name);
|
|
||||||
|
|
||||||
/// \brief Rename the given file, before overwriting it
|
/// \brief Rename the given file, before overwriting it
|
||||||
virtual int backup_file(char const *filename);
|
virtual int backup_file(char const *filename);
|
||||||
|
|
||||||
@ -644,30 +597,49 @@ public:
|
|||||||
return rename_file(filename.c_str(), newfilename.c_str());
|
return rename_file(filename.c_str(), newfilename.c_str());
|
||||||
}
|
}
|
||||||
|
|
||||||
/// \brief Prefix of the input state file
|
/// Prefix of the input state file to be read next
|
||||||
inline std::string & input_prefix()
|
inline std::string & input_prefix()
|
||||||
{
|
{
|
||||||
return input_prefix_str;
|
return input_prefix_str;
|
||||||
}
|
}
|
||||||
|
|
||||||
/// \brief Prefix to be used for output restart files
|
/// Default prefix to be used for all output files (final configuration)
|
||||||
inline std::string & restart_output_prefix()
|
|
||||||
{
|
|
||||||
return restart_output_prefix_str;
|
|
||||||
}
|
|
||||||
|
|
||||||
/// \brief Prefix to be used for output files (final system
|
|
||||||
/// configuration)
|
|
||||||
inline std::string & output_prefix()
|
inline std::string & output_prefix()
|
||||||
{
|
{
|
||||||
return output_prefix_str;
|
return output_prefix_str;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/// Prefix of the restart (checkpoint) file to be written next
|
||||||
|
inline std::string & restart_output_prefix()
|
||||||
|
{
|
||||||
|
return restart_output_prefix_str;
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Default restart frequency (as set by the simulation engine)
|
||||||
|
inline int default_restart_frequency() const
|
||||||
|
{
|
||||||
|
return restart_frequency_engine;
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Buffer from which the input state information may be read
|
||||||
|
inline char const * & input_buffer()
|
||||||
|
{
|
||||||
|
return input_buffer_;
|
||||||
|
}
|
||||||
|
|
||||||
protected:
|
protected:
|
||||||
|
|
||||||
/// \brief Prefix to be used for input files (restarts, not
|
/// Prefix of the input state file to be read next
|
||||||
/// configuration)
|
std::string input_prefix_str;
|
||||||
std::string input_prefix_str, output_prefix_str, restart_output_prefix_str;
|
|
||||||
|
/// Default prefix to be used for all output files (final configuration)
|
||||||
|
std::string output_prefix_str;
|
||||||
|
|
||||||
|
/// Prefix of the restart (checkpoint) file to be written next
|
||||||
|
std::string restart_output_prefix_str;
|
||||||
|
|
||||||
|
/// How often the simulation engine will write its own restart
|
||||||
|
int restart_frequency_engine;
|
||||||
|
|
||||||
/// \brief Currently opened output files: by default, these are ofstream objects.
|
/// \brief Currently opened output files: by default, these are ofstream objects.
|
||||||
/// Allows redefinition to implement different output mechanisms
|
/// Allows redefinition to implement different output mechanisms
|
||||||
@ -675,6 +647,8 @@ protected:
|
|||||||
/// \brief Identifiers for output_stream objects: by default, these are the names of the files
|
/// \brief Identifiers for output_stream objects: by default, these are the names of the files
|
||||||
std::list<std::string> output_stream_names;
|
std::list<std::string> output_stream_names;
|
||||||
|
|
||||||
|
/// Buffer from which the input state information may be read
|
||||||
|
char const *input_buffer_;
|
||||||
};
|
};
|
||||||
|
|
||||||
|
|
||||||
@ -687,6 +661,7 @@ class colvarproxy
|
|||||||
: public colvarproxy_system,
|
: public colvarproxy_system,
|
||||||
public colvarproxy_atoms,
|
public colvarproxy_atoms,
|
||||||
public colvarproxy_atom_groups,
|
public colvarproxy_atom_groups,
|
||||||
|
public colvarproxy_volmaps,
|
||||||
public colvarproxy_smp,
|
public colvarproxy_smp,
|
||||||
public colvarproxy_replicas,
|
public colvarproxy_replicas,
|
||||||
public colvarproxy_script,
|
public colvarproxy_script,
|
||||||
@ -717,6 +692,9 @@ public:
|
|||||||
/// \brief Reset proxy state, e.g. requested atoms
|
/// \brief Reset proxy state, e.g. requested atoms
|
||||||
virtual int reset();
|
virtual int reset();
|
||||||
|
|
||||||
|
/// Close any open files to prevent data loss
|
||||||
|
int close_files();
|
||||||
|
|
||||||
/// (Re)initialize required member data after construction
|
/// (Re)initialize required member data after construction
|
||||||
virtual int setup();
|
virtual int setup();
|
||||||
|
|
||||||
@ -731,14 +709,17 @@ public:
|
|||||||
/// Print a message to the main log
|
/// Print a message to the main log
|
||||||
virtual void log(std::string const &message) = 0;
|
virtual void log(std::string const &message) = 0;
|
||||||
|
|
||||||
/// Print a message to the main log and let the rest of the program handle the error
|
/// Print a message to the main log and/or let the host code know about it
|
||||||
virtual void error(std::string const &message) = 0;
|
virtual void error(std::string const &message) = 0;
|
||||||
|
|
||||||
/// Print a message to the main log and exit with error code
|
/// Record error message (used by VMD to collect them after a script call)
|
||||||
virtual void fatal_error(std::string const &message) = 0;
|
void add_error_msg(std::string const &message);
|
||||||
|
|
||||||
/// \brief Restarts will be written each time this number of steps has passed
|
/// Retrieve accumulated error messages
|
||||||
virtual size_t restart_frequency();
|
std::string const & get_error_msgs();
|
||||||
|
|
||||||
|
/// As the name says
|
||||||
|
void clear_error_msgs();
|
||||||
|
|
||||||
/// Whether a simulation is running (warn against irrecovarable errors)
|
/// Whether a simulation is running (warn against irrecovarable errors)
|
||||||
inline bool simulation_running() const
|
inline bool simulation_running() const
|
||||||
@ -746,6 +727,17 @@ public:
|
|||||||
return b_simulation_running;
|
return b_simulation_running;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/// Is the current step a repetition of a step just executed?
|
||||||
|
/// This is set to true when the step 0 of a new "run" command is being
|
||||||
|
/// executed, regardless of whether a state file has been loaded.
|
||||||
|
inline bool simulation_continuing() const
|
||||||
|
{
|
||||||
|
return b_simulation_continuing;
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Called at the end of a simulation segment (i.e. "run" command)
|
||||||
|
int post_run();
|
||||||
|
|
||||||
/// Convert a version string "YYYY-MM-DD" into an integer
|
/// Convert a version string "YYYY-MM-DD" into an integer
|
||||||
int get_version_from_string(char const *version_string);
|
int get_version_from_string(char const *version_string);
|
||||||
|
|
||||||
@ -755,17 +747,46 @@ public:
|
|||||||
return version_int;
|
return version_int;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/// \brief Returns a reference to the given output channel;
|
||||||
|
/// if this is not open already, then open it
|
||||||
|
virtual std::ostream *output_stream(std::string const &output_name,
|
||||||
|
std::ios_base::openmode mode =
|
||||||
|
std::ios_base::out);
|
||||||
|
|
||||||
|
/// Returns a reference to output_name if it exists, NULL otherwise
|
||||||
|
virtual std::ostream *get_output_stream(std::string const &output_name);
|
||||||
|
|
||||||
|
/// \brief Flushes the given output channel
|
||||||
|
virtual int flush_output_stream(std::ostream *os);
|
||||||
|
|
||||||
|
/// \brief Flushes all output channels
|
||||||
|
virtual int flush_output_streams();
|
||||||
|
|
||||||
|
/// \brief Closes the given output channel
|
||||||
|
virtual int close_output_stream(std::string const &output_name);
|
||||||
|
|
||||||
protected:
|
protected:
|
||||||
|
|
||||||
|
/// Collected error messages
|
||||||
|
std::string error_output;
|
||||||
|
|
||||||
/// Whether a simulation is running (warn against irrecovarable errors)
|
/// Whether a simulation is running (warn against irrecovarable errors)
|
||||||
bool b_simulation_running;
|
bool b_simulation_running;
|
||||||
|
|
||||||
|
/// Is the current step a repetition of a step just executed?
|
||||||
|
/// This is set to true when the step 0 of a new "run" command is being
|
||||||
|
/// executed, regardless of whether a state file has been loaded.
|
||||||
|
bool b_simulation_continuing;
|
||||||
|
|
||||||
/// Whether the entire module should be deallocated by the host engine
|
/// Whether the entire module should be deallocated by the host engine
|
||||||
bool b_delete_requested;
|
bool b_delete_requested;
|
||||||
|
|
||||||
/// Integer representing the version string (allows comparisons)
|
/// Integer representing the version string (allows comparisons)
|
||||||
int version_int;
|
int version_int;
|
||||||
|
|
||||||
|
/// Raise when the output stream functions are used on threads other than 0
|
||||||
|
void smp_stream_error();
|
||||||
|
|
||||||
};
|
};
|
||||||
|
|
||||||
|
|
||||||
|
|||||||
160
lib/colvars/colvarproxy_tcl.cpp
Normal file
160
lib/colvars/colvarproxy_tcl.cpp
Normal file
@ -0,0 +1,160 @@
|
|||||||
|
// -*- c++ -*-
|
||||||
|
|
||||||
|
// This file is part of the Collective Variables module (Colvars).
|
||||||
|
// The original version of Colvars and its updates are located at:
|
||||||
|
// https://github.com/Colvars/colvars
|
||||||
|
// Please update all Colvars source files before making any changes.
|
||||||
|
// If you wish to distribute your changes, please submit them to the
|
||||||
|
// Colvars repository at GitHub.
|
||||||
|
|
||||||
|
#include <sstream>
|
||||||
|
|
||||||
|
#if defined(NAMD_TCL) || defined(VMDTCL)
|
||||||
|
#define COLVARS_TCL
|
||||||
|
#include <tcl.h>
|
||||||
|
#endif
|
||||||
|
|
||||||
|
#include "colvarmodule.h"
|
||||||
|
#include "colvarproxy.h"
|
||||||
|
#include "colvarproxy_tcl.h"
|
||||||
|
#include "colvaratoms.h"
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
colvarproxy_tcl::colvarproxy_tcl()
|
||||||
|
{
|
||||||
|
tcl_interp_ = NULL;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
colvarproxy_tcl::~colvarproxy_tcl()
|
||||||
|
{
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
void colvarproxy_tcl::init_tcl_pointers()
|
||||||
|
{
|
||||||
|
cvm::error("Error: Tcl support is not available in this build.\n",
|
||||||
|
COLVARS_NOT_IMPLEMENTED);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
char const *colvarproxy_tcl::tcl_get_str(void *obj)
|
||||||
|
{
|
||||||
|
#if defined(COLVARS_TCL)
|
||||||
|
return Tcl_GetString(reinterpret_cast<Tcl_Obj *>(obj));
|
||||||
|
#else
|
||||||
|
return NULL;
|
||||||
|
#endif
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int colvarproxy_tcl::tcl_run_force_callback()
|
||||||
|
{
|
||||||
|
#if defined(COLVARS_TCL)
|
||||||
|
Tcl_Interp *const tcl_interp =
|
||||||
|
reinterpret_cast<Tcl_Interp *>(get_tcl_interp());
|
||||||
|
std::string cmd = std::string("calc_colvar_forces ")
|
||||||
|
+ cvm::to_str(cvm::step_absolute());
|
||||||
|
int err = Tcl_Eval(tcl_interp, cmd.c_str());
|
||||||
|
if (err != TCL_OK) {
|
||||||
|
cvm::log(std::string("Error while executing calc_colvar_forces:\n"));
|
||||||
|
cvm::error(Tcl_GetStringResult(tcl_interp));
|
||||||
|
return COLVARS_ERROR;
|
||||||
|
}
|
||||||
|
return cvm::get_error();
|
||||||
|
#else
|
||||||
|
return COLVARS_NOT_IMPLEMENTED;
|
||||||
|
#endif
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int colvarproxy_tcl::tcl_run_colvar_callback(
|
||||||
|
std::string const &name,
|
||||||
|
std::vector<const colvarvalue *> const &cvc_values,
|
||||||
|
colvarvalue &value)
|
||||||
|
{
|
||||||
|
#if defined(COLVARS_TCL)
|
||||||
|
|
||||||
|
Tcl_Interp *const tcl_interp =
|
||||||
|
reinterpret_cast<Tcl_Interp *>(get_tcl_interp());
|
||||||
|
size_t i;
|
||||||
|
std::string cmd = std::string("calc_") + name;
|
||||||
|
for (i = 0; i < cvc_values.size(); i++) {
|
||||||
|
cmd += std::string(" {") + (*(cvc_values[i])).to_simple_string() +
|
||||||
|
std::string("}");
|
||||||
|
}
|
||||||
|
int err = Tcl_Eval(tcl_interp, cmd.c_str());
|
||||||
|
const char *result = Tcl_GetStringResult(tcl_interp);
|
||||||
|
if (err != TCL_OK) {
|
||||||
|
return cvm::error(std::string("Error while executing ")
|
||||||
|
+ cmd + std::string(":\n") +
|
||||||
|
std::string(Tcl_GetStringResult(tcl_interp)),
|
||||||
|
COLVARS_ERROR);
|
||||||
|
}
|
||||||
|
std::istringstream is(result);
|
||||||
|
if (value.from_simple_string(is.str()) != COLVARS_OK) {
|
||||||
|
cvm::log("Error parsing colvar value from script:");
|
||||||
|
cvm::error(result);
|
||||||
|
return COLVARS_ERROR;
|
||||||
|
}
|
||||||
|
return cvm::get_error();
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
return COLVARS_NOT_IMPLEMENTED;
|
||||||
|
|
||||||
|
#endif
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int colvarproxy_tcl::tcl_run_colvar_gradient_callback(
|
||||||
|
std::string const &name,
|
||||||
|
std::vector<const colvarvalue *> const &cvc_values,
|
||||||
|
std::vector<cvm::matrix2d<cvm::real> > &gradient)
|
||||||
|
{
|
||||||
|
#if defined(COLVARS_TCL)
|
||||||
|
|
||||||
|
Tcl_Interp *const tcl_interp =
|
||||||
|
reinterpret_cast<Tcl_Interp *>(get_tcl_interp());
|
||||||
|
size_t i;
|
||||||
|
std::string cmd = std::string("calc_") + name + "_gradient";
|
||||||
|
for (i = 0; i < cvc_values.size(); i++) {
|
||||||
|
cmd += std::string(" {") + (*(cvc_values[i])).to_simple_string() +
|
||||||
|
std::string("}");
|
||||||
|
}
|
||||||
|
int err = Tcl_Eval(tcl_interp, cmd.c_str());
|
||||||
|
if (err != TCL_OK) {
|
||||||
|
return cvm::error(std::string("Error while executing ")
|
||||||
|
+ cmd + std::string(":\n") +
|
||||||
|
std::string(Tcl_GetStringResult(tcl_interp)),
|
||||||
|
COLVARS_ERROR);
|
||||||
|
}
|
||||||
|
Tcl_Obj **list;
|
||||||
|
int n;
|
||||||
|
Tcl_ListObjGetElements(tcl_interp, Tcl_GetObjResult(tcl_interp),
|
||||||
|
&n, &list);
|
||||||
|
if (n != int(gradient.size())) {
|
||||||
|
cvm::error("Error parsing list of gradient values from script: found "
|
||||||
|
+ cvm::to_str(n) + " values instead of " +
|
||||||
|
cvm::to_str(gradient.size()));
|
||||||
|
return COLVARS_ERROR;
|
||||||
|
}
|
||||||
|
for (i = 0; i < gradient.size(); i++) {
|
||||||
|
std::istringstream is(Tcl_GetString(list[i]));
|
||||||
|
if (gradient[i].from_simple_string(is.str()) != COLVARS_OK) {
|
||||||
|
cvm::log("Gradient matrix size: " + cvm::to_str(gradient[i].size()));
|
||||||
|
cvm::log("Gradient string: " + cvm::to_str(Tcl_GetString(list[i])));
|
||||||
|
cvm::error("Error parsing gradient value from script", COLVARS_ERROR);
|
||||||
|
return COLVARS_ERROR;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
return cvm::get_error();
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
return COLVARS_NOT_IMPLEMENTED;
|
||||||
|
|
||||||
|
#endif
|
||||||
|
}
|
||||||
64
lib/colvars/colvarproxy_tcl.h
Normal file
64
lib/colvars/colvarproxy_tcl.h
Normal file
@ -0,0 +1,64 @@
|
|||||||
|
// -*- c++ -*-
|
||||||
|
|
||||||
|
// This file is part of the Collective Variables module (Colvars).
|
||||||
|
// The original version of Colvars and its updates are located at:
|
||||||
|
// https://github.com/Colvars/colvars
|
||||||
|
// Please update all Colvars source files before making any changes.
|
||||||
|
// If you wish to distribute your changes, please submit them to the
|
||||||
|
// Colvars repository at GitHub.
|
||||||
|
|
||||||
|
#ifndef COLVARPROXY_TCL_H
|
||||||
|
#define COLVARPROXY_TCL_H
|
||||||
|
|
||||||
|
#include <vector>
|
||||||
|
|
||||||
|
|
||||||
|
/// Methods for using Tcl within Colvars
|
||||||
|
class colvarproxy_tcl {
|
||||||
|
|
||||||
|
public:
|
||||||
|
|
||||||
|
/// Constructor
|
||||||
|
colvarproxy_tcl();
|
||||||
|
|
||||||
|
/// Destructor
|
||||||
|
virtual ~colvarproxy_tcl();
|
||||||
|
|
||||||
|
/// Is Tcl available? (trigger initialization if needed)
|
||||||
|
int tcl_available();
|
||||||
|
|
||||||
|
/// Tcl implementation of script_obj_to_str()
|
||||||
|
char const *tcl_get_str(void *obj);
|
||||||
|
|
||||||
|
/// Tcl implementation of run_force_callback()
|
||||||
|
int tcl_run_force_callback();
|
||||||
|
|
||||||
|
/// Tcl implementation of run_colvar_callback()
|
||||||
|
int tcl_run_colvar_callback(
|
||||||
|
std::string const &name,
|
||||||
|
std::vector<const colvarvalue *> const &cvcs,
|
||||||
|
colvarvalue &value);
|
||||||
|
|
||||||
|
/// Tcl implementation of run_colvar_gradient_callback()
|
||||||
|
int tcl_run_colvar_gradient_callback(
|
||||||
|
std::string const &name,
|
||||||
|
std::vector<const colvarvalue *> const &cvcs,
|
||||||
|
std::vector<cvm::matrix2d<cvm::real> > &gradient);
|
||||||
|
|
||||||
|
/// Get a pointer to the Tcl interpreter
|
||||||
|
inline void *get_tcl_interp()
|
||||||
|
{
|
||||||
|
return tcl_interp_;
|
||||||
|
}
|
||||||
|
|
||||||
|
protected:
|
||||||
|
|
||||||
|
/// Pointer to Tcl interpreter object
|
||||||
|
void *tcl_interp_;
|
||||||
|
|
||||||
|
/// Set Tcl pointers
|
||||||
|
virtual void init_tcl_pointers();
|
||||||
|
};
|
||||||
|
|
||||||
|
|
||||||
|
#endif
|
||||||
81
lib/colvars/colvarproxy_volmaps.cpp
Normal file
81
lib/colvars/colvarproxy_volmaps.cpp
Normal file
@ -0,0 +1,81 @@
|
|||||||
|
// -*- c++ -*-
|
||||||
|
|
||||||
|
// This file is part of the Collective Variables module (Colvars).
|
||||||
|
// The original version of Colvars and its updates are located at:
|
||||||
|
// https://github.com/Colvars/colvars
|
||||||
|
// Please update all Colvars source files before making any changes.
|
||||||
|
// If you wish to distribute your changes, please submit them to the
|
||||||
|
// Colvars repository at GitHub.
|
||||||
|
|
||||||
|
#include "colvarmodule.h"
|
||||||
|
#include "colvarproxy_volmaps.h"
|
||||||
|
|
||||||
|
|
||||||
|
colvarproxy_volmaps::colvarproxy_volmaps() {}
|
||||||
|
|
||||||
|
|
||||||
|
colvarproxy_volmaps::~colvarproxy_volmaps() {}
|
||||||
|
|
||||||
|
|
||||||
|
int colvarproxy_volmaps::volmaps_available()
|
||||||
|
{
|
||||||
|
return COLVARS_NOT_IMPLEMENTED;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int colvarproxy_volmaps::reset()
|
||||||
|
{
|
||||||
|
for (size_t i = 0; i < volmaps_ids.size(); i++) {
|
||||||
|
clear_volmap(i);
|
||||||
|
}
|
||||||
|
volmaps_ids.clear();
|
||||||
|
volmaps_ncopies.clear();
|
||||||
|
volmaps_values.clear();
|
||||||
|
volmaps_new_colvar_forces.clear();
|
||||||
|
return COLVARS_OK;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int colvarproxy_volmaps::add_volmap_slot(int volmap_id)
|
||||||
|
{
|
||||||
|
volmaps_ids.push_back(volmap_id);
|
||||||
|
volmaps_ncopies.push_back(1);
|
||||||
|
volmaps_values.push_back(0.0);
|
||||||
|
volmaps_new_colvar_forces.push_back(0.0);
|
||||||
|
return (volmaps_ids.size() - 1);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int colvarproxy_volmaps::init_volmap(int volmap_id)
|
||||||
|
{
|
||||||
|
return cvm::error("Error: access to volumetric maps is unavailable "
|
||||||
|
"in this build.\n",
|
||||||
|
COLVARS_NOT_IMPLEMENTED);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int colvarproxy_volmaps::init_volmap(const char *volmap_name)
|
||||||
|
{
|
||||||
|
return cvm::error("Error: access to volumetric maps is unavailable "
|
||||||
|
"in this build.\n",
|
||||||
|
COLVARS_NOT_IMPLEMENTED);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int colvarproxy_volmaps::init_volmap(const std::string &volmap_name)
|
||||||
|
{
|
||||||
|
return init_volmap(volmap_name.c_str());
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
void colvarproxy_volmaps::clear_volmap(int index)
|
||||||
|
{
|
||||||
|
if (((size_t) index) >= volmaps_ids.size()) {
|
||||||
|
cvm::error("Error: trying to unrequest a volumetric map that was not "
|
||||||
|
"previously requested.\n", INPUT_ERROR);
|
||||||
|
}
|
||||||
|
|
||||||
|
if (volmaps_ncopies[index] > 0) {
|
||||||
|
volmaps_ncopies[index] -= 1;
|
||||||
|
}
|
||||||
|
}
|
||||||
76
lib/colvars/colvarproxy_volmaps.h
Normal file
76
lib/colvars/colvarproxy_volmaps.h
Normal file
@ -0,0 +1,76 @@
|
|||||||
|
// -*- c++ -*-
|
||||||
|
|
||||||
|
#ifndef COLVARPROXY_VOLMAPS_H
|
||||||
|
#define COLVARPROXY_VOLMAPS_H
|
||||||
|
|
||||||
|
|
||||||
|
/// \brief Container of grid-based objects
|
||||||
|
class colvarproxy_volmaps {
|
||||||
|
|
||||||
|
public:
|
||||||
|
|
||||||
|
/// Contructor
|
||||||
|
colvarproxy_volmaps();
|
||||||
|
|
||||||
|
/// Destructor
|
||||||
|
virtual ~colvarproxy_volmaps();
|
||||||
|
|
||||||
|
/// Clear volumetric map data
|
||||||
|
int reset();
|
||||||
|
|
||||||
|
/// \brief Whether this implementation has capability to use volumetric maps
|
||||||
|
virtual int volmaps_available();
|
||||||
|
|
||||||
|
/// Create a slot for a volumetric map not requested yet
|
||||||
|
int add_volmap_slot(int volmap_id);
|
||||||
|
|
||||||
|
/// Request and prepare this volumetric map for use by Colvars
|
||||||
|
virtual int init_volmap(int volmap_id);
|
||||||
|
|
||||||
|
/// Request and prepare this volumetric map for use by Colvars
|
||||||
|
virtual int init_volmap(char const *volmap_name);
|
||||||
|
|
||||||
|
/// Request and prepare this volumetric map for use by Colvars
|
||||||
|
int init_volmap(std::string const &volmap_name);
|
||||||
|
|
||||||
|
/// \brief Used by the CVC destructors
|
||||||
|
virtual void clear_volmap(int index);
|
||||||
|
|
||||||
|
/// Get the numeric ID of the given volumetric map (for the MD program)
|
||||||
|
inline int get_volmap_id(int index) const
|
||||||
|
{
|
||||||
|
return volmaps_ids[index];
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Read the current value of the volumetric map
|
||||||
|
inline cvm::real get_volmap_value(int index) const
|
||||||
|
{
|
||||||
|
return volmaps_values[index];
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Request that this force is applied to the given volumetric map
|
||||||
|
inline void apply_volmap_force(int index, cvm::real const &new_force)
|
||||||
|
{
|
||||||
|
volmaps_new_colvar_forces[index] += new_force;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
protected:
|
||||||
|
|
||||||
|
/// \brief Array of numeric IDs of volumetric maps
|
||||||
|
std::vector<int> volmaps_ids;
|
||||||
|
|
||||||
|
/// \brief Keep track of how many times each vol map is used by a
|
||||||
|
/// separate colvar object
|
||||||
|
std::vector<size_t> volmaps_ncopies;
|
||||||
|
|
||||||
|
/// \brief Current values of the vol maps
|
||||||
|
std::vector<cvm::real> volmaps_values;
|
||||||
|
|
||||||
|
/// \brief Forces applied from colvars, to be communicated to the MD
|
||||||
|
/// integrator
|
||||||
|
std::vector<cvm::real> volmaps_new_colvar_forces;
|
||||||
|
};
|
||||||
|
|
||||||
|
|
||||||
|
#endif
|
||||||
@ -1,3 +1,3 @@
|
|||||||
#ifndef COLVARS_VERSION
|
#ifndef COLVARS_VERSION
|
||||||
#define COLVARS_VERSION "2020-02-25"
|
#define COLVARS_VERSION "2020-07-07"
|
||||||
#endif
|
#endif
|
||||||
|
|||||||
File diff suppressed because it is too large
Load Diff
@ -8,7 +8,7 @@
|
|||||||
// Colvars repository at GitHub.
|
// Colvars repository at GitHub.
|
||||||
|
|
||||||
#ifndef COLVARSCRIPT_H
|
#ifndef COLVARSCRIPT_H
|
||||||
//#define COLVARSCRIPT_H // Delay definition until later
|
#define COLVARSCRIPT_H
|
||||||
|
|
||||||
#include <string>
|
#include <string>
|
||||||
#include <vector>
|
#include <vector>
|
||||||
@ -29,7 +29,7 @@ class colvarscript {
|
|||||||
|
|
||||||
private:
|
private:
|
||||||
|
|
||||||
colvarproxy *proxy;
|
colvarproxy *proxy_;
|
||||||
colvarmodule *colvars;
|
colvarmodule *colvars;
|
||||||
|
|
||||||
inline colvarscript() {} // no-argument construction forbidden
|
inline colvarscript() {} // no-argument construction forbidden
|
||||||
@ -38,8 +38,9 @@ public:
|
|||||||
|
|
||||||
friend class colvarproxy;
|
friend class colvarproxy;
|
||||||
|
|
||||||
colvarscript(colvarproxy * p);
|
colvarscript(colvarproxy *p);
|
||||||
inline ~colvarscript() {}
|
|
||||||
|
~colvarscript();
|
||||||
|
|
||||||
/// If an error is caught by the proxy through fatal_error(), this is set to
|
/// If an error is caught by the proxy through fatal_error(), this is set to
|
||||||
/// COLVARSCRIPT_ERROR
|
/// COLVARSCRIPT_ERROR
|
||||||
@ -49,112 +50,196 @@ public:
|
|||||||
/// error message
|
/// error message
|
||||||
std::string result;
|
std::string result;
|
||||||
|
|
||||||
/// Run script command with given positional arguments (objects)
|
/// Run a script command with space-separated positional arguments (objects)
|
||||||
int run(int objc, unsigned char *const objv[]);
|
int run(int objc, unsigned char *const objv[]);
|
||||||
|
|
||||||
/// Set the return value of the script command to the given string
|
/// Get the string result of the current scripting call
|
||||||
inline void set_str_result(std::string const &s)
|
inline std::string const &str_result() const
|
||||||
{
|
{
|
||||||
result = s;
|
return result;
|
||||||
}
|
}
|
||||||
|
|
||||||
/// Build and return a short help
|
/// Modify the string result of the current scripting call
|
||||||
std::string help_string(void) const;
|
inline std::string &modify_str_result()
|
||||||
|
{
|
||||||
|
return result;
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Set the return value to the given string
|
||||||
|
int set_result_str(std::string const &s);
|
||||||
|
|
||||||
|
/// Clear the string result
|
||||||
|
int clear_str_result();
|
||||||
|
|
||||||
|
/// Add the given string to the error message of the script interface
|
||||||
|
void add_error_msg(std::string const &s);
|
||||||
|
|
||||||
|
/// Commands available
|
||||||
|
enum command {
|
||||||
|
#define CVSCRIPT_ENUM_COMM(COMM) COMM,
|
||||||
|
#undef CVSCRIPT
|
||||||
|
#define CVSCRIPT(COMM,HELP,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY) \
|
||||||
|
CVSCRIPT_ENUM_COMM(COMM)
|
||||||
|
#ifdef COLVARSCRIPT_COMMANDS_H
|
||||||
|
#undef COLVARSCRIPT_COMMANDS_H
|
||||||
|
#endif
|
||||||
|
#include "colvarscript_commands.h"
|
||||||
|
#undef COLVARSCRIPT_COMMANDS_H
|
||||||
|
#undef CVSCRIPT
|
||||||
|
#undef CVSCRIPT_ENUM_COMM
|
||||||
|
cv_n_commands
|
||||||
|
};
|
||||||
|
|
||||||
|
/// Type of object handling a script command
|
||||||
|
enum Object_type {
|
||||||
|
use_module,
|
||||||
|
use_colvar,
|
||||||
|
use_bias
|
||||||
|
};
|
||||||
|
|
||||||
|
/// Return the prefix of the individual command for each object function
|
||||||
|
std::string get_cmd_prefix(Object_type t);
|
||||||
|
|
||||||
|
/// Get a pointer to the i-th argument of the command (NULL if not given)
|
||||||
|
template<Object_type T>
|
||||||
|
unsigned char *get_cmd_arg(int iarg, int objc, unsigned char *const objv[]);
|
||||||
|
|
||||||
|
/// Instantiation of get_cmd_arg<> for module-level commands
|
||||||
|
unsigned char *get_module_cmd_arg(int iarg, int objc,
|
||||||
|
unsigned char *const objv[]);
|
||||||
|
|
||||||
|
/// Instantiation of get_cmd_arg<> for colvar-level commands
|
||||||
|
unsigned char *get_colvar_cmd_arg(int iarg, int objc,
|
||||||
|
unsigned char *const objv[]);
|
||||||
|
|
||||||
|
/// Instantiation of get_cmd_arg<> for bias-level commands
|
||||||
|
unsigned char *get_bias_cmd_arg(int iarg, int objc,
|
||||||
|
unsigned char *const objv[]);
|
||||||
|
|
||||||
|
/// Check the argument count of the command
|
||||||
|
template<Object_type T>
|
||||||
|
int check_cmd_nargs(char const *cmd, int objc,
|
||||||
|
int n_args_min, int n_args_max);
|
||||||
|
|
||||||
|
/// Instantiation of check_cmd_nargs<> for module-level commands
|
||||||
|
int check_module_cmd_nargs(char const *cmd, int objc,
|
||||||
|
int n_args_min, int n_args_max);
|
||||||
|
|
||||||
|
/// Instantiation of check_cmd_nargs<> for colvar-level commands
|
||||||
|
int check_colvar_cmd_nargs(char const *cmd, int objc,
|
||||||
|
int n_args_min, int n_args_max);
|
||||||
|
|
||||||
|
/// Instantiation of get_cmd_arg<> for bias-level commands
|
||||||
|
int check_bias_cmd_nargs(char const *cmd, int objc,
|
||||||
|
int n_args_min, int n_args_max);
|
||||||
|
|
||||||
|
/// Number of positional arguments to shift for each object type
|
||||||
|
template<colvarscript::Object_type T>
|
||||||
|
int cmd_arg_shift();
|
||||||
|
|
||||||
/// Use scripting language to get the string representation of an object
|
/// Use scripting language to get the string representation of an object
|
||||||
inline char const *obj_to_str(unsigned char *const obj)
|
inline char const *obj_to_str(unsigned char *const obj)
|
||||||
{
|
{
|
||||||
return cvm::proxy->script_obj_to_str(obj);
|
return (obj == NULL ? NULL : proxy_->script_obj_to_str(obj));
|
||||||
}
|
}
|
||||||
|
|
||||||
enum command {
|
/// Get names of all commands
|
||||||
cv_help,
|
inline char const **get_command_names() const
|
||||||
cv_version,
|
{
|
||||||
cv_config,
|
return cmd_names;
|
||||||
cv_getconfig,
|
}
|
||||||
cv_configfile,
|
|
||||||
cv_reset,
|
/// Get help string for a command (does not specify how it is launched)
|
||||||
cv_resetindexgroups,
|
/// \param cmd Name of the command's function (e.g. "cv_units")
|
||||||
cv_delete,
|
std::string get_command_help(char const *cmd);
|
||||||
cv_list,
|
|
||||||
cv_list_biases,
|
/// Get summary of command line syntax for all commands of a given context
|
||||||
cv_load,
|
/// \param t One of use_module, use_colvar or use_bias
|
||||||
cv_save,
|
std::string get_cmdline_help_summary(Object_type t);
|
||||||
cv_update,
|
|
||||||
cv_addenergy,
|
/// Get a description of how the command should be used in a command line
|
||||||
cv_getenergy,
|
/// \param t One of use_module, use_colvar or use_bias
|
||||||
cv_printframe,
|
/// \param c Value of the \link command \endlink enum
|
||||||
cv_printframelabels,
|
std::string get_command_cmdline_syntax(Object_type t, command c);
|
||||||
cv_frame,
|
|
||||||
cv_units,
|
/// Get the command line syntax following by the help string
|
||||||
cv_colvar,
|
/// \param t One of use_module, use_colvar or use_bias
|
||||||
cv_colvar_value,
|
/// \param cmd Name of the subcommand (e.g. "units")
|
||||||
cv_colvar_update,
|
std::string get_command_cmdline_help(Object_type t, std::string const &cmd);
|
||||||
cv_colvar_type,
|
|
||||||
cv_colvar_delete,
|
/// Set error code for unsupported script operation
|
||||||
cv_colvar_addforce,
|
int unsupported_op();
|
||||||
cv_colvar_getappliedforce,
|
|
||||||
cv_colvar_gettotalforce,
|
/// Pointer to the Colvars main object
|
||||||
cv_colvar_cvcflags,
|
inline colvarmodule *module()
|
||||||
cv_colvar_getconfig,
|
{
|
||||||
cv_colvar_get,
|
return this->colvars;
|
||||||
cv_colvar_set,
|
}
|
||||||
cv_bias,
|
|
||||||
cv_bias_energy,
|
/// Pointer to the colvarproxy object (interface with host engine)
|
||||||
cv_bias_update,
|
inline colvarproxy *proxy()
|
||||||
cv_bias_delete,
|
{
|
||||||
cv_bias_getconfig,
|
return this->proxy_;
|
||||||
cv_bias_get,
|
}
|
||||||
cv_bias_set,
|
|
||||||
cv_n_commands
|
private:
|
||||||
};
|
|
||||||
|
/// Set up all script API functions
|
||||||
|
int init_commands();
|
||||||
|
|
||||||
|
/// Set up a single script API function
|
||||||
|
int init_command(colvarscript::command const &comm,
|
||||||
|
char const *name, char const *help,
|
||||||
|
int n_args_min, int n_args_max, char const *arghelp,
|
||||||
|
int (*fn)(void *, int, unsigned char * const *));
|
||||||
|
|
||||||
/// Execute a script command
|
/// Execute a script command
|
||||||
inline int exec_command(command c,
|
inline int exec_command(command c,
|
||||||
void *pobj,
|
void *pobj,
|
||||||
int objc, unsigned char * const *objv)
|
int objc, unsigned char * const *objv)
|
||||||
{
|
{
|
||||||
return (*(comm_fns[c]))(pobj, objc, objv);
|
return (*(cmd_fns[c]))(pobj, objc, objv);
|
||||||
}
|
}
|
||||||
|
|
||||||
/// Get help for a command (TODO reformat for each language?)
|
public: // TODO this function will be removed soon
|
||||||
inline std::string command_help(colvarscript::command c) const
|
|
||||||
{
|
|
||||||
return comm_help[c];
|
|
||||||
}
|
|
||||||
|
|
||||||
/// Clear all object results
|
|
||||||
inline void clear_results()
|
|
||||||
{
|
|
||||||
result.clear();
|
|
||||||
}
|
|
||||||
|
|
||||||
private:
|
|
||||||
|
|
||||||
/// Run subcommands on colvar
|
|
||||||
int proc_colvar(colvar *cv, int argc, unsigned char *const argv[]);
|
|
||||||
|
|
||||||
/// Run subcommands on bias
|
|
||||||
int proc_bias(colvarbias *b, int argc, unsigned char *const argv[]);
|
|
||||||
|
|
||||||
/// Run subcommands on base colvardeps object (colvar, bias, ...)
|
/// Run subcommands on base colvardeps object (colvar, bias, ...)
|
||||||
int proc_features(colvardeps *obj,
|
int proc_features(colvardeps *obj,
|
||||||
int argc, unsigned char *const argv[]);
|
int argc, unsigned char *const argv[]);
|
||||||
|
|
||||||
|
private: // TODO
|
||||||
|
|
||||||
/// Internal identifiers of command strings
|
/// Internal identifiers of command strings
|
||||||
std::map<std::string, command> comm_str_map;
|
std::map<std::string, command> cmd_str_map;
|
||||||
|
|
||||||
|
/// Inverse of cmd_str_map (to be exported outside this class)
|
||||||
|
char const **cmd_names;
|
||||||
|
|
||||||
/// Help strings for each command
|
/// Help strings for each command
|
||||||
std::vector<std::string> comm_help;
|
std::vector<std::string> cmd_help;
|
||||||
|
|
||||||
/// Number of arguments for each command
|
/// Minimum number of arguments for each command
|
||||||
std::vector<size_t> comm_n_args;
|
std::vector<size_t> cmd_n_args_min;
|
||||||
|
|
||||||
/// Arguments for each command
|
/// Maximum number of arguments for each command
|
||||||
std::vector< std::vector<std::string> > comm_args;
|
std::vector<size_t> cmd_n_args_max;
|
||||||
|
|
||||||
|
/// Help strings for each command argument
|
||||||
|
std::vector< std::vector<std::string> > cmd_arghelp;
|
||||||
|
|
||||||
/// Implementations of each command
|
/// Implementations of each command
|
||||||
std::vector<int (*)(void *, int, unsigned char * const *)> comm_fns;
|
std::vector<int (*)(void *, int, unsigned char * const *)> cmd_fns;
|
||||||
|
|
||||||
|
/// Get a pointer to the implementation of the given command
|
||||||
|
inline int (*get_cmd_fn(std::string const &cmd_key))(void *,
|
||||||
|
int,
|
||||||
|
unsigned char * const *)
|
||||||
|
{
|
||||||
|
if (cmd_str_map.count(cmd_key) > 0) {
|
||||||
|
return cmd_fns[cmd_str_map[cmd_key]];
|
||||||
|
}
|
||||||
|
return NULL;
|
||||||
|
}
|
||||||
|
|
||||||
};
|
};
|
||||||
|
|
||||||
@ -165,12 +250,14 @@ inline static colvarscript *colvarscript_obj()
|
|||||||
return cvm::main()->proxy->script;
|
return cvm::main()->proxy->script;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
/// Get a pointer to the colvar object pointed to by pobj
|
/// Get a pointer to the colvar object pointed to by pobj
|
||||||
inline static colvar *colvar_obj(void *pobj)
|
inline static colvar *colvar_obj(void *pobj)
|
||||||
{
|
{
|
||||||
return reinterpret_cast<colvar *>(pobj);
|
return reinterpret_cast<colvar *>(pobj);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
/// Get a pointer to the colvarbias object pointed to by pobj
|
/// Get a pointer to the colvarbias object pointed to by pobj
|
||||||
inline static colvarbias *colvarbias_obj(void *pobj)
|
inline static colvarbias *colvarbias_obj(void *pobj)
|
||||||
{
|
{
|
||||||
@ -178,137 +265,124 @@ inline static colvarbias *colvarbias_obj(void *pobj)
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
#define CVSCRIPT_COMM_FNAME(COMM) cvscript_ ## COMM
|
|
||||||
|
|
||||||
#define CVSCRIPT_COMM_PROTO(COMM) \
|
template<colvarscript::Object_type T>
|
||||||
int CVSCRIPT_COMM_FNAME(COMM)(void *, int, unsigned char *const *);
|
unsigned char *colvarscript::get_cmd_arg(int iarg,
|
||||||
|
int objc,
|
||||||
#define CVSCRIPT(COMM,HELP,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY) \
|
unsigned char *const objv[])
|
||||||
CVSCRIPT_COMM_PROTO(COMM)
|
{
|
||||||
|
int const shift = cmd_arg_shift<T>();
|
||||||
#undef COLVARSCRIPT_H
|
return (shift+iarg < objc) ? objv[shift+iarg] : NULL;
|
||||||
#endif // #ifndef COLVARSCRIPT_H
|
}
|
||||||
|
|
||||||
|
|
||||||
#ifdef COLVARSCRIPT_CPP
|
inline unsigned char *colvarscript::get_module_cmd_arg(int iarg, int objc,
|
||||||
#define CVSCRIPT_COMM_FN(COMM,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY) \
|
unsigned char *const objv[])
|
||||||
extern "C" int CVSCRIPT_COMM_FNAME(COMM)(void *pobj, \
|
{
|
||||||
int objc, \
|
return get_cmd_arg<use_module>(iarg, objc, objv);
|
||||||
unsigned char *const objv[]) \
|
}
|
||||||
{ \
|
|
||||||
colvarscript *script = colvarscript_obj(); \
|
|
||||||
script->clear_results(); \
|
|
||||||
if (objc < 2+N_ARGS_MIN) /* "cv" and "COMM" are 1st and 2nd */ { \
|
|
||||||
script->set_str_result("Missing arguments\n" + \
|
|
||||||
script->command_help(colvarscript::COMM)); \
|
|
||||||
return COLVARSCRIPT_ERROR; \
|
|
||||||
} \
|
|
||||||
if (objc > 2+N_ARGS_MAX) { \
|
|
||||||
script->set_str_result("Too many arguments\n" + \
|
|
||||||
script->command_help(colvarscript::COMM)); \
|
|
||||||
return COLVARSCRIPT_ERROR; \
|
|
||||||
} \
|
|
||||||
FN_BODY; \
|
|
||||||
}
|
|
||||||
#undef CVSCRIPT
|
|
||||||
#define CVSCRIPT(COMM,HELP,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY) \
|
|
||||||
CVSCRIPT_COMM_FN(COMM,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY)
|
|
||||||
#endif // #ifdef COLVARSCRIPT_CPP
|
|
||||||
|
|
||||||
|
|
||||||
#ifdef COLVARSCRIPT_INIT_FN
|
inline unsigned char *colvarscript::get_colvar_cmd_arg(int iarg, int objc,
|
||||||
#define CVSCRIPT_COMM_INIT(COMM,HELP,ARGS) { \
|
unsigned char *const objv[])
|
||||||
comm_str_map[#COMM] = COMM; \
|
{
|
||||||
comm_help[COMM] = HELP; \
|
return get_cmd_arg<use_colvar>(iarg, objc, objv);
|
||||||
comm_fns[COMM] = &(CVSCRIPT_COMM_FNAME(COMM)); \
|
}
|
||||||
}
|
|
||||||
#undef CVSCRIPT
|
|
||||||
#define CVSCRIPT(COMM,HELP,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY) \
|
|
||||||
CVSCRIPT_COMM_INIT(COMM,HELP,ARGS)
|
|
||||||
#endif
|
|
||||||
|
|
||||||
|
|
||||||
#if !defined(COLVARSCRIPT_H) || defined(COLVARSCRIPT_INIT_FN)
|
inline unsigned char *colvarscript::get_bias_cmd_arg(int iarg, int objc,
|
||||||
#define COLVARSCRIPT_H
|
unsigned char *const objv[])
|
||||||
|
{
|
||||||
|
return get_cmd_arg<use_bias>(iarg, objc, objv);
|
||||||
|
}
|
||||||
|
|
||||||
#ifndef COLVARSCRIPT_INIT_FN
|
|
||||||
#ifdef __cplusplus
|
|
||||||
extern "C" {
|
|
||||||
#endif
|
|
||||||
#endif
|
|
||||||
|
|
||||||
// Add optional arguments for command-specific help?
|
template<colvarscript::Object_type T>
|
||||||
CVSCRIPT(cv_help,
|
int colvarscript::check_cmd_nargs(char const *cmd,
|
||||||
"Print the help message",
|
int objc,
|
||||||
0, 0,
|
int n_args_min,
|
||||||
{},
|
int n_args_max)
|
||||||
script->set_str_result(script->help_string());
|
{
|
||||||
return COLVARS_OK;
|
int const shift = cmd_arg_shift<T>();
|
||||||
)
|
if (objc < shift+n_args_min) {
|
||||||
|
add_error_msg("Missing arguments for script function \""+std::string(cmd)+
|
||||||
CVSCRIPT(cv_config,
|
"\":\n"+get_command_help(cmd));
|
||||||
"Read configuration from the given string",
|
|
||||||
1, 1,
|
|
||||||
{ "conf (str) - Configuration string" },
|
|
||||||
std::string const conf(script->obj_to_str(objv[2]));
|
|
||||||
if (cvm::main()->read_config_string(conf) == COLVARS_OK) {
|
|
||||||
return COLVARS_OK;
|
|
||||||
}
|
|
||||||
script->set_str_result("Error parsing configuration string");
|
|
||||||
return COLVARSCRIPT_ERROR;
|
return COLVARSCRIPT_ERROR;
|
||||||
)
|
|
||||||
|
|
||||||
CVSCRIPT(cv_getconfig,
|
|
||||||
"Get the module's configuration string read so far",
|
|
||||||
0, 0,
|
|
||||||
{ },
|
|
||||||
script->set_str_result(cvm::main()->get_config());
|
|
||||||
return COLVARS_OK;
|
|
||||||
)
|
|
||||||
|
|
||||||
CVSCRIPT(cv_resetindexgroups,
|
|
||||||
"Clear the index groups loaded so far, allowing to replace them",
|
|
||||||
0, 0,
|
|
||||||
{ },
|
|
||||||
return cvm::main()->reset_index_groups();
|
|
||||||
)
|
|
||||||
|
|
||||||
CVSCRIPT(cv_addenergy,
|
|
||||||
"Add an energy to the MD engine",
|
|
||||||
1, 1,
|
|
||||||
{ "E (float) - Amount of energy to add" },
|
|
||||||
cvm::main()->total_bias_energy +=
|
|
||||||
strtod(script->obj_to_str(objv[2]), NULL);
|
|
||||||
return COLVARS_OK;
|
|
||||||
)
|
|
||||||
|
|
||||||
CVSCRIPT(cv_getenergy,
|
|
||||||
"Get the current Colvars energy",
|
|
||||||
1, 1,
|
|
||||||
{ "E (float) - Store the energy in this variable" },
|
|
||||||
double *energy = reinterpret_cast<double *>(objv[2]);
|
|
||||||
*energy = cvm::main()->total_bias_energy;
|
|
||||||
return COLVARS_OK;
|
|
||||||
)
|
|
||||||
|
|
||||||
CVSCRIPT(cv_units,
|
|
||||||
"Get the current Colvars unit system",
|
|
||||||
0, 1,
|
|
||||||
{ },
|
|
||||||
if (objc < 3) {
|
|
||||||
script->set_str_result(cvm::proxy->units);
|
|
||||||
return COLVARS_OK;
|
|
||||||
} else {
|
|
||||||
return cvm::proxy->set_unit_system(script->obj_to_str(objv[2]) , false);
|
|
||||||
}
|
}
|
||||||
)
|
if (objc > shift+n_args_max) {
|
||||||
|
add_error_msg("Too many arguments for script function \""+std::string(cmd)+
|
||||||
|
"\":\n"+get_command_help(cmd));
|
||||||
|
return COLVARSCRIPT_ERROR;
|
||||||
|
}
|
||||||
|
return COLVARSCRIPT_OK;
|
||||||
|
}
|
||||||
|
|
||||||
#ifndef COLVARSCRIPT_INIT_FN
|
|
||||||
#ifdef __cplusplus
|
|
||||||
} // extern "C"
|
|
||||||
#endif
|
|
||||||
#endif
|
|
||||||
|
|
||||||
#undef CVSCRIPT
|
inline int colvarscript::check_module_cmd_nargs(char const *cmd,
|
||||||
|
int objc,
|
||||||
|
int n_args_min,
|
||||||
|
int n_args_max)
|
||||||
|
{
|
||||||
|
return check_cmd_nargs<use_module>(cmd, objc, n_args_min, n_args_max);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
inline int colvarscript::check_colvar_cmd_nargs(char const *cmd,
|
||||||
|
int objc,
|
||||||
|
int n_args_min,
|
||||||
|
int n_args_max)
|
||||||
|
{
|
||||||
|
return check_cmd_nargs<use_colvar>(cmd, objc, n_args_min, n_args_max);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
inline int colvarscript::check_bias_cmd_nargs(char const *cmd,
|
||||||
|
int objc,
|
||||||
|
int n_args_min,
|
||||||
|
int n_args_max)
|
||||||
|
{
|
||||||
|
return check_cmd_nargs<use_bias>(cmd, objc, n_args_min, n_args_max);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
template<colvarscript::Object_type T>
|
||||||
|
int colvarscript::cmd_arg_shift()
|
||||||
|
{
|
||||||
|
int shift = 0;
|
||||||
|
if (T == use_module) {
|
||||||
|
// "cv" and "COMMAND" are 1st and 2nd argument, and shift is equal to 2
|
||||||
|
shift = 2;
|
||||||
|
} else if (T == use_colvar) {
|
||||||
|
// Same as above with additional arguments "colvar" and "NAME"
|
||||||
|
shift = 4;
|
||||||
|
} else if (T == use_bias) {
|
||||||
|
shift = 4;
|
||||||
|
}
|
||||||
|
return shift;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
extern "C" {
|
||||||
|
|
||||||
|
#if defined(COLVARS_TCL)
|
||||||
|
/// Run the script API via Tcl command-line interface
|
||||||
|
/// \param clientData Not used
|
||||||
|
/// \param my_interp Pointer to Tcl_Interp object (read from Colvars if NULL)
|
||||||
|
/// \param objc Number of Tcl command parameters
|
||||||
|
/// \param objv Array of command parameters
|
||||||
|
/// \return Result of the script command
|
||||||
|
int tcl_run_colvarscript_command(ClientData clientData,
|
||||||
|
Tcl_Interp *interp_in,
|
||||||
|
int objc, Tcl_Obj *const objv[]);
|
||||||
|
#endif // #if defined(COLVARS_TCL)
|
||||||
|
|
||||||
|
/// Generic wrapper for string-based scripting
|
||||||
|
int run_colvarscript_command(int objc, unsigned char *const objv[]);
|
||||||
|
|
||||||
|
/// Get the string result of a script call
|
||||||
|
const char * get_colvarscript_result();
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
#endif // #ifndef COLVARSCRIPT_H
|
#endif // #ifndef COLVARSCRIPT_H
|
||||||
|
|||||||
65
lib/colvars/colvarscript_commands.cpp
Normal file
65
lib/colvars/colvarscript_commands.cpp
Normal file
@ -0,0 +1,65 @@
|
|||||||
|
// -*- c++ -*-
|
||||||
|
|
||||||
|
// This file is part of the Collective Variables module (Colvars).
|
||||||
|
// The original version of Colvars and its updates are located at:
|
||||||
|
// https://github.com/Colvars/colvars
|
||||||
|
// Please update all Colvars source files before making any changes.
|
||||||
|
// If you wish to distribute your changes, please submit them to the
|
||||||
|
// Colvars repository at GitHub.
|
||||||
|
|
||||||
|
#include <vector>
|
||||||
|
#include <cstdlib>
|
||||||
|
#include <string.h>
|
||||||
|
|
||||||
|
#include "colvarproxy.h"
|
||||||
|
#include "colvardeps.h"
|
||||||
|
#include "colvarscript.h"
|
||||||
|
#include "colvarscript_commands.h"
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
extern "C"
|
||||||
|
int cvscript_n_commands()
|
||||||
|
{
|
||||||
|
return static_cast<int>(colvarscript::cv_n_commands);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
extern "C"
|
||||||
|
char const **cvscript_command_names()
|
||||||
|
{
|
||||||
|
colvarscript *script = colvarscript_obj();
|
||||||
|
return script->get_command_names();
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
// Instantiate the body of all script commands
|
||||||
|
|
||||||
|
#define CVSCRIPT_COMM_FN(COMM,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY) \
|
||||||
|
int CVSCRIPT_COMM_FNAME(COMM)(void *pobj, \
|
||||||
|
int objc, unsigned char *const objv[]) \
|
||||||
|
{ \
|
||||||
|
if (cvm::debug()) { \
|
||||||
|
cvm::log("Executing script function \""+std::string(#COMM)+"\""); \
|
||||||
|
} \
|
||||||
|
colvarscript *script = colvarscript_obj(); \
|
||||||
|
script->clear_str_result(); \
|
||||||
|
if (script->check_module_cmd_nargs(#COMM, \
|
||||||
|
objc, N_ARGS_MIN, N_ARGS_MAX) != \
|
||||||
|
COLVARSCRIPT_OK) { \
|
||||||
|
return COLVARSCRIPT_ERROR; \
|
||||||
|
} \
|
||||||
|
FN_BODY; \
|
||||||
|
}
|
||||||
|
#undef CVSCRIPT
|
||||||
|
#define CVSCRIPT(COMM,HELP,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY) \
|
||||||
|
CVSCRIPT_COMM_FN(COMM,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY)
|
||||||
|
|
||||||
|
// Skips the colvar- and bias- specific commands
|
||||||
|
#define COLVARSCRIPT_COMMANDS_GLOBAL
|
||||||
|
|
||||||
|
#undef COLVARSCRIPT_COMMANDS_H
|
||||||
|
#include "colvarscript_commands.h"
|
||||||
|
|
||||||
|
#undef CVSCRIPT_COMM_FN
|
||||||
|
#undef CVSCRIPT
|
||||||
407
lib/colvars/colvarscript_commands.h
Normal file
407
lib/colvars/colvarscript_commands.h
Normal file
@ -0,0 +1,407 @@
|
|||||||
|
// -*- c++ -*-
|
||||||
|
|
||||||
|
// This file is part of the Collective Variables module (Colvars).
|
||||||
|
// The original version of Colvars and its updates are located at:
|
||||||
|
// https://github.com/Colvars/colvars
|
||||||
|
// Please update all Colvars source files before making any changes.
|
||||||
|
// If you wish to distribute your changes, please submit them to the
|
||||||
|
// Colvars repository at GitHub.
|
||||||
|
|
||||||
|
#ifndef COLVARSCRIPT_COMMANDS_H
|
||||||
|
#define COLVARSCRIPT_COMMANDS_H
|
||||||
|
|
||||||
|
// The following is a complete definition of the scripting API.
|
||||||
|
|
||||||
|
// The CVSCRIPT macro is used in four distinct contexts:
|
||||||
|
// 1) Expand to the functions' prototypes (when included generically)
|
||||||
|
// 2) List colvarscript::command entries (when included in colvarscript.h)
|
||||||
|
// 3) Implement colvarscript::init() (when included in colvarscript.cpp)
|
||||||
|
// 4) Define the functions' bodies (when included in colvarscript_commands.cpp)
|
||||||
|
|
||||||
|
|
||||||
|
// Each command is created by an instance of the CVSCRIPT macro
|
||||||
|
|
||||||
|
// The arguments of the CVSCRIPT macro are:
|
||||||
|
|
||||||
|
// COMM = the id of the command (must be a member of colvarscript::command)
|
||||||
|
|
||||||
|
// HELP = a one-line description (C string literal) for the command
|
||||||
|
|
||||||
|
// N_ARGS_MIN = the lowest number of arguments allowed
|
||||||
|
|
||||||
|
// N_ARGS_MAX = the highest number of arguments allowed
|
||||||
|
|
||||||
|
// ARGS = multi-line string literal describing each parameter; each line
|
||||||
|
// follows the format "name : type - description"
|
||||||
|
|
||||||
|
// FN_BODY = the implementation of the function; this should be a thin wrapper
|
||||||
|
// over existing functions; the "script" pointer to the colvarscript
|
||||||
|
// object is already set by the CVSCRIPT_COMM_FN macro; see also the
|
||||||
|
// functions in colvarscript_commands.h.
|
||||||
|
|
||||||
|
#ifndef CVSCRIPT_COMM_FNAME
|
||||||
|
#define CVSCRIPT_COMM_FNAME(COMM) cvscript_ ## COMM
|
||||||
|
#endif
|
||||||
|
|
||||||
|
// If CVSCRIPT is not defined, this file yields the function prototypes
|
||||||
|
#ifndef CVSCRIPT
|
||||||
|
|
||||||
|
#ifdef __cplusplus
|
||||||
|
#define CVSCRIPT_COMM_PROTO(COMM) \
|
||||||
|
extern "C" int CVSCRIPT_COMM_FNAME(COMM)(void *, \
|
||||||
|
int, unsigned char *const *);
|
||||||
|
#else
|
||||||
|
#define CVSCRIPT_COMM_PROTO(COMM) \
|
||||||
|
int CVSCRIPT_COMM_FNAME(COMM)(void *, int, unsigned char *const *);
|
||||||
|
#endif
|
||||||
|
|
||||||
|
#define CVSCRIPT(COMM,HELP,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY) \
|
||||||
|
CVSCRIPT_COMM_PROTO(COMM)
|
||||||
|
|
||||||
|
|
||||||
|
// Utility functions used to query the command database
|
||||||
|
extern "C" {
|
||||||
|
|
||||||
|
/// Get the number of colvarscript commands
|
||||||
|
int cvscript_n_commands();
|
||||||
|
|
||||||
|
/// Get the names of all commands (array of strings)
|
||||||
|
char const ** cvscript_command_names();
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
|
||||||
|
|
||||||
|
CVSCRIPT(cv_addenergy,
|
||||||
|
"Add an energy to the MD engine (no effect in VMD)",
|
||||||
|
1, 1,
|
||||||
|
"E : float - Amount of energy to add",
|
||||||
|
char const *Earg =
|
||||||
|
script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
|
||||||
|
cvm::main()->total_bias_energy += strtod(Earg, NULL);
|
||||||
|
return cvm::get_error(); // TODO Make this multi-language
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(cv_bias,
|
||||||
|
"Prefix for bias-specific commands",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
// This cannot be executed from a command line
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(cv_colvar,
|
||||||
|
"Prefix for colvar-specific commands",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
// This cannot be executed from a command line
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(cv_config,
|
||||||
|
"Read configuration from the given string",
|
||||||
|
1, 1,
|
||||||
|
"conf : string - Configuration string",
|
||||||
|
char const *conf_str =
|
||||||
|
script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
|
||||||
|
std::string const conf(conf_str);
|
||||||
|
if (cvm::main()->read_config_string(conf) == COLVARS_OK) {
|
||||||
|
return COLVARS_OK;
|
||||||
|
}
|
||||||
|
script->add_error_msg("Error parsing configuration string");
|
||||||
|
return COLVARSCRIPT_ERROR;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(cv_configfile,
|
||||||
|
"Read configuration from a file",
|
||||||
|
1, 1,
|
||||||
|
"conf_file : string - Path to configuration file",
|
||||||
|
char const *conf_file_name =
|
||||||
|
script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
|
||||||
|
if (script->module()->read_config_file(conf_file_name) == COLVARS_OK) {
|
||||||
|
return COLVARS_OK;
|
||||||
|
} else {
|
||||||
|
script->add_error_msg("Error parsing configuration file");
|
||||||
|
return COLVARSCRIPT_ERROR;
|
||||||
|
}
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(cv_delete,
|
||||||
|
"Delete this Colvars module instance (VMD only)",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
return script->proxy()->request_deletion();
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(cv_frame,
|
||||||
|
"Get or set current frame number (VMD only)",
|
||||||
|
0, 1,
|
||||||
|
"frame : integer - Frame number",
|
||||||
|
char const *arg =
|
||||||
|
script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
|
||||||
|
if (arg == NULL) {
|
||||||
|
long int f = -1;
|
||||||
|
if (script->proxy()->get_frame(f) == COLVARS_OK) {
|
||||||
|
script->set_result_str(cvm::to_str(f));
|
||||||
|
return COLVARS_OK;
|
||||||
|
} else {
|
||||||
|
script->add_error_msg("Frame number is not available");
|
||||||
|
return COLVARSCRIPT_ERROR;
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
int const f = strtol(const_cast<char *>(arg), NULL, 10);
|
||||||
|
int error_code = script->proxy()->set_frame(f);
|
||||||
|
if (error_code == COLVARS_NO_SUCH_FRAME) {
|
||||||
|
script->add_error_msg("Invalid frame number: \""+std::string(arg)+
|
||||||
|
"\"\n");
|
||||||
|
}
|
||||||
|
return error_code;
|
||||||
|
}
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(cv_getconfig,
|
||||||
|
"Get the module's configuration string read so far",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
script->set_result_str(cvm::main()->get_config());
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(cv_getenergy,
|
||||||
|
"Get the current Colvars energy",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
script->set_result_str(cvm::to_str(cvm::main()->total_bias_energy));
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(cv_help,
|
||||||
|
"Get the help string of the Colvars scripting interface",
|
||||||
|
0, 1,
|
||||||
|
"command : string - Get the help string of this specific command",
|
||||||
|
unsigned char *const cmdobj =
|
||||||
|
script->get_module_cmd_arg(0, objc, objv);
|
||||||
|
if (cmdobj) {
|
||||||
|
std::string const cmdstr(script->obj_to_str(cmdobj));
|
||||||
|
if (cmdstr.size()) {
|
||||||
|
if (cmdstr == std::string("colvar")) {
|
||||||
|
script->set_result_str(script->get_cmdline_help_summary(colvarscript::use_colvar));
|
||||||
|
} else if (cmdstr == std::string("bias")) {
|
||||||
|
script->set_result_str(script->get_cmdline_help_summary(colvarscript::use_bias));
|
||||||
|
} else {
|
||||||
|
script->set_result_str(script->get_command_cmdline_help(colvarscript::use_module,
|
||||||
|
cmdstr));
|
||||||
|
}
|
||||||
|
return cvm::get_error();
|
||||||
|
} else {
|
||||||
|
return COLVARSCRIPT_ERROR;
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
script->set_result_str(script->get_cmdline_help_summary(colvarscript::use_module));
|
||||||
|
return COLVARS_OK;
|
||||||
|
}
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(cv_list,
|
||||||
|
"Return a list of all variables or biases",
|
||||||
|
0, 1,
|
||||||
|
"param : string - \"colvars\" or \"biases\"; default is \"colvars\"",
|
||||||
|
std::string res;
|
||||||
|
unsigned char *const kwarg = script->get_module_cmd_arg(0, objc, objv);
|
||||||
|
std::string const kwstr = kwarg ? script->obj_to_str(kwarg) :
|
||||||
|
std::string("colvars");
|
||||||
|
if (kwstr == "colvars") {
|
||||||
|
for (std::vector<colvar *>::iterator cvi = script->module()->variables()->begin();
|
||||||
|
cvi != script->module()->variables()->end();
|
||||||
|
++cvi) {
|
||||||
|
res += (cvi == script->module()->variables()->begin() ? "" : " ") + (*cvi)->name;
|
||||||
|
}
|
||||||
|
script->set_result_str(res);
|
||||||
|
return COLVARS_OK;
|
||||||
|
} else if (kwstr == "biases") {
|
||||||
|
for (std::vector<colvarbias *>::iterator bi = script->module()->biases.begin();
|
||||||
|
bi != script->module()->biases.end();
|
||||||
|
++bi) {
|
||||||
|
res += (bi == script->module()->biases.begin() ? "" : " ") + (*bi)->name;
|
||||||
|
}
|
||||||
|
script->set_result_str(res);
|
||||||
|
return COLVARS_OK;
|
||||||
|
} else {
|
||||||
|
script->add_error_msg("Wrong arguments to command \"list\"\n");
|
||||||
|
return COLVARSCRIPT_ERROR;
|
||||||
|
}
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(cv_listcommands,
|
||||||
|
"Get the list of script functions, prefixed with \"cv_\", \"colvar_\" or \"bias_\"",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
int const n_commands = cvscript_n_commands();
|
||||||
|
char const **command_names = cvscript_command_names();
|
||||||
|
std::string result;
|
||||||
|
for (int i = 0; i < n_commands; i++) {
|
||||||
|
if (i > 0) result.append(1, ' ');
|
||||||
|
result.append(std::string(command_names[i]));
|
||||||
|
}
|
||||||
|
script->set_result_str(result);
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(cv_load,
|
||||||
|
"Load data from a state file into all matching colvars and biases",
|
||||||
|
1, 1,
|
||||||
|
"prefix : string - Path to existing state file or input prefix",
|
||||||
|
char const *arg =
|
||||||
|
script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
|
||||||
|
script->proxy()->input_prefix() = cvm::state_file_prefix(arg);
|
||||||
|
if (script->module()->setup_input() == COLVARS_OK) {
|
||||||
|
return COLVARS_OK;
|
||||||
|
} else {
|
||||||
|
script->add_error_msg("Error loading state file");
|
||||||
|
return COLVARSCRIPT_ERROR;
|
||||||
|
}
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(cv_loadfromstring,
|
||||||
|
"Load state data from a string into all matching colvars and biases",
|
||||||
|
1, 1,
|
||||||
|
"buffer : string - String buffer containing the state information",
|
||||||
|
char const *arg =
|
||||||
|
script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
|
||||||
|
script->proxy()->input_buffer() = arg;
|
||||||
|
if (script->module()->setup_input() == COLVARS_OK) {
|
||||||
|
return COLVARS_OK;
|
||||||
|
} else {
|
||||||
|
script->add_error_msg("Error loading state string");
|
||||||
|
return COLVARSCRIPT_ERROR;
|
||||||
|
}
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(cv_molid,
|
||||||
|
"Get or set the molecule ID on which Colvars is defined (VMD only)",
|
||||||
|
0, 1,
|
||||||
|
"molid : integer - Molecule ID; -1 means undefined",
|
||||||
|
char const *arg =
|
||||||
|
script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
|
||||||
|
if (arg == NULL) {
|
||||||
|
int molid = -1;
|
||||||
|
script->proxy()->get_molid(molid);
|
||||||
|
script->set_result_str(cvm::to_str(molid));
|
||||||
|
return COLVARS_OK;
|
||||||
|
} else {
|
||||||
|
script->add_error_msg("Error: To change the molecule ID in VMD, use cv delete first.");
|
||||||
|
return COLVARS_NOT_IMPLEMENTED;
|
||||||
|
}
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(cv_printframe,
|
||||||
|
"Return the values that would be written to colvars.traj",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
std::ostringstream os;
|
||||||
|
script->module()->write_traj(os);
|
||||||
|
script->set_result_str(os.str());
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(cv_printframelabels,
|
||||||
|
"Return the labels that would be written to colvars.traj",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
std::ostringstream os;
|
||||||
|
script->module()->write_traj_label(os);
|
||||||
|
script->set_result_str(os.str());
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(cv_reset,
|
||||||
|
"Delete all internal configuration",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
return script->module()->reset();
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(cv_resetindexgroups,
|
||||||
|
"Clear the index groups loaded so far, allowing to replace them",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
cvm::main()->index_group_names.clear();
|
||||||
|
cvm::main()->index_groups.clear();
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(cv_save,
|
||||||
|
"Change the prefix of all output files and save them",
|
||||||
|
1, 1,
|
||||||
|
"prefix : string - Output prefix with trailing \".colvars.state\" gets removed)",
|
||||||
|
std::string const prefix =
|
||||||
|
cvm::state_file_prefix(script->obj_to_str(script->get_module_cmd_arg(0, objc, objv)));
|
||||||
|
script->proxy()->output_prefix() = prefix;
|
||||||
|
int error_code = COLVARS_OK;
|
||||||
|
error_code |= script->module()->setup_output();
|
||||||
|
error_code |= script->module()->write_restart_file(prefix+
|
||||||
|
".colvars.state");
|
||||||
|
error_code |= script->module()->write_output_files();
|
||||||
|
return error_code;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(cv_savetostring,
|
||||||
|
"Write the Colvars state to a string and return it",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
return script->module()->write_restart_string(script->modify_str_result());
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(cv_units,
|
||||||
|
"Get or set the current Colvars unit system",
|
||||||
|
0, 1,
|
||||||
|
"units : string - The new unit system",
|
||||||
|
char const *argstr =
|
||||||
|
script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
|
||||||
|
if (argstr) {
|
||||||
|
return cvm::proxy->set_unit_system(argstr, false);
|
||||||
|
} else {
|
||||||
|
script->set_result_str(cvm::proxy->units);
|
||||||
|
return COLVARS_OK;
|
||||||
|
}
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(cv_update,
|
||||||
|
"Recalculate colvars and biases",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
int error_code = script->proxy()->update_input();
|
||||||
|
if (error_code) {
|
||||||
|
script->add_error_msg("Error updating the Colvars module (input)");
|
||||||
|
return error_code;
|
||||||
|
}
|
||||||
|
error_code |= script->module()->calc();
|
||||||
|
if (error_code) {
|
||||||
|
script->add_error_msg("Error updating the Colvars module (calc)");
|
||||||
|
return error_code;
|
||||||
|
}
|
||||||
|
error_code |= script->proxy()->update_output();
|
||||||
|
if (error_code) {
|
||||||
|
script->add_error_msg("Error updating the Colvars module (output)");
|
||||||
|
}
|
||||||
|
return error_code;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(cv_version,
|
||||||
|
"Get the Colvars Module version number",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
script->set_result_str(COLVARS_VERSION);
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
// This guard allows compiling colvar and bias function bodies in their
|
||||||
|
// respecitve files instead of colvarscript_commands.o
|
||||||
|
#ifndef COLVARSCRIPT_COMMANDS_GLOBAL
|
||||||
|
#include "colvarscript_commands_colvar.h"
|
||||||
|
#include "colvarscript_commands_bias.h"
|
||||||
|
#endif
|
||||||
|
|
||||||
|
#endif // #ifndef COLVARSCRIPT_COMMANDS_H
|
||||||
49
lib/colvars/colvarscript_commands_bias.cpp
Normal file
49
lib/colvars/colvarscript_commands_bias.cpp
Normal file
@ -0,0 +1,49 @@
|
|||||||
|
// -*- c++ -*-
|
||||||
|
|
||||||
|
// This file is part of the Collective Variables module (Colvars).
|
||||||
|
// The original version of Colvars and its updates are located at:
|
||||||
|
// https://github.com/Colvars/colvars
|
||||||
|
// Please update all Colvars source files before making any changes.
|
||||||
|
// If you wish to distribute your changes, please submit them to the
|
||||||
|
// Colvars repository at GitHub.
|
||||||
|
|
||||||
|
|
||||||
|
#include <vector>
|
||||||
|
#include <cstdlib>
|
||||||
|
#include <stdlib.h>
|
||||||
|
#include <string.h>
|
||||||
|
|
||||||
|
#include "colvarproxy.h"
|
||||||
|
#include "colvardeps.h"
|
||||||
|
#include "colvarscript.h"
|
||||||
|
#include "colvarscript_commands.h"
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
// Instantiate the body of all bias-specific script commands
|
||||||
|
|
||||||
|
#define CVSCRIPT_COMM_FN(COMM,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY) \
|
||||||
|
int CVSCRIPT_COMM_FNAME(COMM)(void *pobj, \
|
||||||
|
int objc, unsigned char *const objv[]) \
|
||||||
|
{ \
|
||||||
|
if (cvm::debug()) { \
|
||||||
|
cvm::log("Executing script function \""+std::string(#COMM)+"\""); \
|
||||||
|
} \
|
||||||
|
colvarscript *script = colvarscript_obj(); \
|
||||||
|
script->clear_str_result(); \
|
||||||
|
if (script->check_bias_cmd_nargs(#COMM, \
|
||||||
|
objc, N_ARGS_MIN, N_ARGS_MAX) != \
|
||||||
|
COLVARSCRIPT_OK) { \
|
||||||
|
return COLVARSCRIPT_ERROR; \
|
||||||
|
} \
|
||||||
|
colvarbias *this_bias = colvarbias_obj(pobj); \
|
||||||
|
FN_BODY; \
|
||||||
|
}
|
||||||
|
#undef CVSCRIPT
|
||||||
|
#define CVSCRIPT(COMM,HELP,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY) \
|
||||||
|
CVSCRIPT_COMM_FN(COMM,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY)
|
||||||
|
|
||||||
|
#include "colvarscript_commands_bias.h"
|
||||||
|
|
||||||
|
#undef CVSCRIPT_COMM_FN
|
||||||
|
#undef CVSCRIPT
|
||||||
173
lib/colvars/colvarscript_commands_bias.h
Normal file
173
lib/colvars/colvarscript_commands_bias.h
Normal file
@ -0,0 +1,173 @@
|
|||||||
|
// -*- c++ -*-
|
||||||
|
|
||||||
|
// This file is part of the Collective Variables module (Colvars).
|
||||||
|
// The original version of Colvars and its updates are located at:
|
||||||
|
// https://github.com/Colvars/colvars
|
||||||
|
// Please update all Colvars source files before making any changes.
|
||||||
|
// If you wish to distribute your changes, please submit them to the
|
||||||
|
// Colvars repository at GitHub.
|
||||||
|
|
||||||
|
|
||||||
|
CVSCRIPT(bias_bin,
|
||||||
|
"Get the current grid bin index (1D ABF only for now)",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
script->set_result_str(cvm::to_str(this_bias->current_bin()));
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(bias_bincount,
|
||||||
|
"Get the number of samples at the given grid bin (1D ABF only for now)",
|
||||||
|
0, 1,
|
||||||
|
"index : integer - Grid index; defaults to current bin",
|
||||||
|
int index = this_bias->current_bin();
|
||||||
|
char const *indexarg =
|
||||||
|
script->obj_to_str(script->get_bias_cmd_arg(0, objc, objv));
|
||||||
|
if (indexarg) {
|
||||||
|
std::string const param(indexarg);
|
||||||
|
if (!(std::istringstream(param) >> index)) {
|
||||||
|
script->add_error_msg("bincount: error parsing bin index");
|
||||||
|
return COLVARSCRIPT_ERROR;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
script->set_result_str(cvm::to_str(this_bias->bin_count(index)));
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(bias_binnum,
|
||||||
|
"Get the total number of grid points of this bias (1D ABF only for now)",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
int r = this_bias->bin_num();
|
||||||
|
if (r < 0) {
|
||||||
|
script->add_error_msg("Error: calling bin_num() for bias " +
|
||||||
|
this_bias->name);
|
||||||
|
return COLVARSCRIPT_ERROR;
|
||||||
|
}
|
||||||
|
script->set_result_str(cvm::to_str(r));
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(bias_delete,
|
||||||
|
"Delete this bias",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
delete this_bias;
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(bias_energy,
|
||||||
|
"Get the current energy of this bias",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
script->set_result_str(cvm::to_str(this_bias->get_energy()));
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(bias_get,
|
||||||
|
"Get the value of the given feature for this bias",
|
||||||
|
1, 1,
|
||||||
|
"feature : string - Name of the feature",
|
||||||
|
return script->proc_features(this_bias, objc, objv);
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(bias_getconfig,
|
||||||
|
"Return the configuration string of this bias",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
script->set_result_str(this_bias->get_config());
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(bias_help,
|
||||||
|
"Get a help summary or the help string of one bias subcommand",
|
||||||
|
0, 1,
|
||||||
|
"command : string - Get the help string of this specific command",
|
||||||
|
unsigned char *const cmdobj =
|
||||||
|
script->get_colvar_cmd_arg(0, objc, objv);
|
||||||
|
if (this_bias) {
|
||||||
|
}
|
||||||
|
if (cmdobj) {
|
||||||
|
std::string const cmdstr(script->obj_to_str(cmdobj));
|
||||||
|
if (cmdstr.size()) {
|
||||||
|
script->set_result_str(script->get_command_cmdline_help(colvarscript::use_bias,
|
||||||
|
cmdstr));
|
||||||
|
return COLVARS_OK;
|
||||||
|
} else {
|
||||||
|
return COLVARSCRIPT_ERROR;
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
script->set_result_str(script->get_cmdline_help_summary(colvarscript::use_bias));
|
||||||
|
return COLVARS_OK;
|
||||||
|
}
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(bias_load,
|
||||||
|
"Load data into this bias",
|
||||||
|
1, 1,
|
||||||
|
"prefix : string - Read from a file with this name or prefix",
|
||||||
|
char const *arg =
|
||||||
|
script->obj_to_str(script->get_bias_cmd_arg(0, objc, objv));
|
||||||
|
return this_bias->read_state_prefix(std::string(arg));
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(bias_loadfromstring,
|
||||||
|
"Load state data into this bias from a string",
|
||||||
|
1, 1,
|
||||||
|
"buffer : string - String buffer containing the state information",
|
||||||
|
char const *buffer = script->obj_to_str(script->get_bias_cmd_arg(0, objc, objv));
|
||||||
|
return this_bias->read_state_string(buffer);
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(bias_save,
|
||||||
|
"Save data from this bias into a file with the given prefix",
|
||||||
|
1, 1,
|
||||||
|
"prefix : string - Prefix for the state file of this bias",
|
||||||
|
std::string const prefix =
|
||||||
|
cvm::state_file_prefix(script->obj_to_str(script->get_bias_cmd_arg(0, objc, objv)));
|
||||||
|
return this_bias->write_state_prefix(prefix);
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(bias_savetostring,
|
||||||
|
"Save data from this bias into a string and return it",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
return this_bias->write_state_string(script->modify_str_result());
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(bias_set,
|
||||||
|
"Set the given feature of this bias to a new value",
|
||||||
|
2, 2,
|
||||||
|
"feature : string - Name of the feature\n"
|
||||||
|
"value : string - String representation of the new feature value",
|
||||||
|
return script->proc_features(this_bias, objc, objv);
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(bias_share,
|
||||||
|
"Share bias information with other replicas (multiple-walker scheme)",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
if (this_bias->replica_share() != COLVARS_OK) {
|
||||||
|
script->add_error_msg("Error: calling replica_share() for bias " +
|
||||||
|
this_bias->name);
|
||||||
|
return COLVARSCRIPT_ERROR;
|
||||||
|
}
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(bias_state,
|
||||||
|
"Print a string representation of the feature state of this bias",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
this_bias->print_state();
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(bias_update,
|
||||||
|
"Recompute this bias and return its up-to-date energy",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
this_bias->update();
|
||||||
|
script->set_result_str(cvm::to_str(this_bias->get_energy()));
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
49
lib/colvars/colvarscript_commands_colvar.cpp
Normal file
49
lib/colvars/colvarscript_commands_colvar.cpp
Normal file
@ -0,0 +1,49 @@
|
|||||||
|
// -*- c++ -*-
|
||||||
|
|
||||||
|
// This file is part of the Collective Variables module (Colvars).
|
||||||
|
// The original version of Colvars and its updates are located at:
|
||||||
|
// https://github.com/Colvars/colvars
|
||||||
|
// Please update all Colvars source files before making any changes.
|
||||||
|
// If you wish to distribute your changes, please submit them to the
|
||||||
|
// Colvars repository at GitHub.
|
||||||
|
|
||||||
|
|
||||||
|
#include <vector>
|
||||||
|
#include <cstdlib>
|
||||||
|
#include <stdlib.h>
|
||||||
|
#include <string.h>
|
||||||
|
|
||||||
|
#include "colvarproxy.h"
|
||||||
|
#include "colvardeps.h"
|
||||||
|
#include "colvarscript.h"
|
||||||
|
#include "colvarscript_commands.h"
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
// Instantiate the body of all colvar-specific script commands
|
||||||
|
|
||||||
|
#define CVSCRIPT_COMM_FN(COMM,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY) \
|
||||||
|
int CVSCRIPT_COMM_FNAME(COMM)(void *pobj, \
|
||||||
|
int objc, unsigned char *const objv[]) \
|
||||||
|
{ \
|
||||||
|
if (cvm::debug()) { \
|
||||||
|
cvm::log("Executing script function \""+std::string(#COMM)+"\""); \
|
||||||
|
} \
|
||||||
|
colvarscript *script = colvarscript_obj(); \
|
||||||
|
script->clear_str_result(); \
|
||||||
|
if (script->check_colvar_cmd_nargs(#COMM, \
|
||||||
|
objc, N_ARGS_MIN, N_ARGS_MAX) != \
|
||||||
|
COLVARSCRIPT_OK) { \
|
||||||
|
return COLVARSCRIPT_ERROR; \
|
||||||
|
} \
|
||||||
|
colvar *this_colvar = colvar_obj(pobj); \
|
||||||
|
FN_BODY; \
|
||||||
|
}
|
||||||
|
#undef CVSCRIPT
|
||||||
|
#define CVSCRIPT(COMM,HELP,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY) \
|
||||||
|
CVSCRIPT_COMM_FN(COMM,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY)
|
||||||
|
|
||||||
|
#include "colvarscript_commands_colvar.h"
|
||||||
|
|
||||||
|
#undef CVSCRIPT_COMM_FN
|
||||||
|
#undef CVSCRIPT
|
||||||
239
lib/colvars/colvarscript_commands_colvar.h
Normal file
239
lib/colvars/colvarscript_commands_colvar.h
Normal file
@ -0,0 +1,239 @@
|
|||||||
|
// -*- c++ -*-
|
||||||
|
|
||||||
|
// This file is part of the Collective Variables module (Colvars).
|
||||||
|
// The original version of Colvars and its updates are located at:
|
||||||
|
// https://github.com/Colvars/colvars
|
||||||
|
// Please update all Colvars source files before making any changes.
|
||||||
|
// If you wish to distribute your changes, please submit them to the
|
||||||
|
// Colvars repository at GitHub.
|
||||||
|
|
||||||
|
|
||||||
|
CVSCRIPT(colvar_addforce,
|
||||||
|
"Apply the given force onto this colvar and return the same",
|
||||||
|
1, 1,
|
||||||
|
"force : float or array - Applied force; must match colvar dimensionality",
|
||||||
|
std::string const f_str(script->obj_to_str(script->get_colvar_cmd_arg(0, objc, objv)));
|
||||||
|
std::istringstream is(f_str);
|
||||||
|
is.width(cvm::cv_width);
|
||||||
|
is.precision(cvm::cv_prec);
|
||||||
|
colvarvalue force(this_colvar->value());
|
||||||
|
force.is_derivative();
|
||||||
|
if (force.from_simple_string(is.str()) != COLVARS_OK) {
|
||||||
|
script->add_error_msg("addforce : error parsing force value");
|
||||||
|
return COLVARSCRIPT_ERROR;
|
||||||
|
}
|
||||||
|
this_colvar->add_bias_force(force);
|
||||||
|
script->set_result_str(force.to_simple_string());
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(colvar_cvcflags,
|
||||||
|
"Enable or disable individual components by setting their active flags",
|
||||||
|
1, 1,
|
||||||
|
"flags : integer array - Zero/nonzero value disables/enables the CVC",
|
||||||
|
std::string const flags_str(script->obj_to_str(script->get_colvar_cmd_arg(0, objc, objv)));
|
||||||
|
std::istringstream is(flags_str);
|
||||||
|
std::vector<bool> flags;
|
||||||
|
int flag;
|
||||||
|
while (is >> flag) {
|
||||||
|
flags.push_back(flag != 0);
|
||||||
|
}
|
||||||
|
int res = this_colvar->set_cvc_flags(flags);
|
||||||
|
if (res != COLVARS_OK) {
|
||||||
|
script->add_error_msg("Error setting CVC flags");
|
||||||
|
return COLVARSCRIPT_ERROR;
|
||||||
|
}
|
||||||
|
script->set_result_str("0");
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(colvar_delete,
|
||||||
|
"Delete this colvar, along with all biases that depend on it",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
delete this_colvar;
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(colvar_get,
|
||||||
|
"Get the value of the given feature for this colvar",
|
||||||
|
1, 1,
|
||||||
|
"feature : string - Name of the feature",
|
||||||
|
return script->proc_features(this_colvar, objc, objv);
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(colvar_getappliedforce,
|
||||||
|
"Return the total of the forces applied to this colvar",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
script->set_result_str((this_colvar->applied_force()).to_simple_string());
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(colvar_getatomgroups,
|
||||||
|
"Return the atom indices used by this colvar as a list of lists",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
std::string result;
|
||||||
|
std::vector<std::vector<int> > lists = this_colvar->get_atom_lists();
|
||||||
|
std::vector<std::vector<int> >::iterator li = lists.begin();
|
||||||
|
for ( ; li != lists.end(); ++li) {
|
||||||
|
result += "{";
|
||||||
|
std::vector<int>::iterator lj = (*li).begin();
|
||||||
|
for ( ; lj != (*li).end(); ++lj) {
|
||||||
|
result += cvm::to_str(*lj);
|
||||||
|
result += " ";
|
||||||
|
}
|
||||||
|
result += "} ";
|
||||||
|
}
|
||||||
|
script->set_result_str(result);
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(colvar_getatomids,
|
||||||
|
"Return the list of atom indices used by this colvar",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
std::string result;
|
||||||
|
std::vector<int>::iterator li = this_colvar->atom_ids.begin();
|
||||||
|
for ( ; li != this_colvar->atom_ids.end(); ++li) {
|
||||||
|
result += cvm::to_str(*li);
|
||||||
|
result += " ";
|
||||||
|
}
|
||||||
|
script->set_result_str(result);
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(colvar_getconfig,
|
||||||
|
"Return the configuration string of this colvar",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
script->set_result_str(this_colvar->get_config());
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(colvar_getgradients,
|
||||||
|
"Return the atomic gradients of this colvar",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
std::string result;
|
||||||
|
std::vector<cvm::rvector>::iterator li =
|
||||||
|
this_colvar->atomic_gradients.begin();
|
||||||
|
for ( ; li != this_colvar->atomic_gradients.end(); ++li) {
|
||||||
|
result += "{";
|
||||||
|
int j;
|
||||||
|
for (j = 0; j < 3; ++j) {
|
||||||
|
result += cvm::to_str((*li)[j]);
|
||||||
|
result += " ";
|
||||||
|
}
|
||||||
|
result += "} ";
|
||||||
|
}
|
||||||
|
script->set_result_str(result);
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(colvar_gettotalforce,
|
||||||
|
"Return the sum of internal and external forces to this colvar",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
script->set_result_str((this_colvar->total_force()).to_simple_string());
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(colvar_help,
|
||||||
|
"Get a help summary or the help string of one colvar subcommand",
|
||||||
|
0, 1,
|
||||||
|
"command : string - Get the help string of this specific command",
|
||||||
|
unsigned char *const cmdobj =
|
||||||
|
script->get_colvar_cmd_arg(0, objc, objv);
|
||||||
|
if (this_colvar) {
|
||||||
|
}
|
||||||
|
if (cmdobj) {
|
||||||
|
std::string const cmdstr(script->obj_to_str(cmdobj));
|
||||||
|
if (cmdstr.size()) {
|
||||||
|
script->set_result_str(script->get_command_cmdline_help(colvarscript::use_colvar,
|
||||||
|
cmdstr));
|
||||||
|
return cvm::get_error();
|
||||||
|
} else {
|
||||||
|
return COLVARSCRIPT_ERROR;
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
script->set_result_str(script->get_cmdline_help_summary(colvarscript::use_colvar));
|
||||||
|
return COLVARS_OK;
|
||||||
|
}
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(colvar_modifycvcs,
|
||||||
|
"Modify configuration of individual components by passing string arguments",
|
||||||
|
1, 1,
|
||||||
|
"confs : sequence of strings - New configurations; empty strings are skipped",
|
||||||
|
std::vector<std::string> const confs(script->proxy()->script_obj_to_str_vector(script->get_colvar_cmd_arg(0, objc, objv)));
|
||||||
|
cvm::increase_depth();
|
||||||
|
int res = this_colvar->update_cvc_config(confs);
|
||||||
|
cvm::decrease_depth();
|
||||||
|
if (res != COLVARS_OK) {
|
||||||
|
script->add_error_msg("Error setting CVC flags");
|
||||||
|
return COLVARSCRIPT_ERROR;
|
||||||
|
}
|
||||||
|
script->set_result_str("0");
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(colvar_run_ave,
|
||||||
|
"Get the current running average of the value of this colvar",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
script->set_result_str(this_colvar->run_ave().to_simple_string());
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(colvar_set,
|
||||||
|
"Set the given feature of this colvar to a new value",
|
||||||
|
2, 2,
|
||||||
|
"feature : string - Name of the feature\n"
|
||||||
|
"value : string - String representation of the new feature value",
|
||||||
|
return script->proc_features(this_colvar, objc, objv);
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(colvar_state,
|
||||||
|
"Print a string representation of the feature state of this colvar",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
this_colvar->print_state();
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(colvar_type,
|
||||||
|
"Get the type description of this colvar",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
script->set_result_str(this_colvar->value().type_desc(this_colvar->value().value_type));
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(colvar_update,
|
||||||
|
"Recompute this colvar and return its up-to-date value",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
this_colvar->calc();
|
||||||
|
this_colvar->update_forces_energy();
|
||||||
|
script->set_result_str((this_colvar->value()).to_simple_string());
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(colvar_value,
|
||||||
|
"Get the current value of this colvar",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
script->set_result_str(this_colvar->value().to_simple_string());
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
|
|
||||||
|
CVSCRIPT(colvar_width,
|
||||||
|
"Get the width of this colvar",
|
||||||
|
0, 0,
|
||||||
|
"",
|
||||||
|
script->set_result_str(cvm::to_str(this_colvar->width, 0,
|
||||||
|
cvm::cv_prec));
|
||||||
|
return COLVARS_OK;
|
||||||
|
)
|
||||||
@ -74,7 +74,7 @@ std::ostream & operator << (std::ostream &os, colvarmodule::rvector const &v)
|
|||||||
|
|
||||||
std::istream & operator >> (std::istream &is, colvarmodule::rvector &v)
|
std::istream & operator >> (std::istream &is, colvarmodule::rvector &v)
|
||||||
{
|
{
|
||||||
size_t const start_pos = is.tellg();
|
std::streampos const start_pos = is.tellg();
|
||||||
char sep;
|
char sep;
|
||||||
if ( !(is >> sep) || !(sep == '(') ||
|
if ( !(is >> sep) || !(sep == '(') ||
|
||||||
!(is >> v.x) || !(is >> sep) || !(sep == ',') ||
|
!(is >> v.x) || !(is >> sep) || !(sep == ',') ||
|
||||||
@ -130,7 +130,7 @@ std::ostream & operator << (std::ostream &os, colvarmodule::quaternion const &q)
|
|||||||
|
|
||||||
std::istream & operator >> (std::istream &is, colvarmodule::quaternion &q)
|
std::istream & operator >> (std::istream &is, colvarmodule::quaternion &q)
|
||||||
{
|
{
|
||||||
size_t const start_pos = is.tellg();
|
std::streampos const start_pos = is.tellg();
|
||||||
|
|
||||||
std::string euler("");
|
std::string euler("");
|
||||||
|
|
||||||
|
|||||||
@ -270,7 +270,7 @@ public:
|
|||||||
cvm::vector1d<T> &v)
|
cvm::vector1d<T> &v)
|
||||||
{
|
{
|
||||||
if (v.size() == 0) return is;
|
if (v.size() == 0) return is;
|
||||||
size_t const start_pos = is.tellg();
|
std::streampos const start_pos = is.tellg();
|
||||||
char sep;
|
char sep;
|
||||||
if ( !(is >> sep) || !(sep == '(') ) {
|
if ( !(is >> sep) || !(sep == '(') ) {
|
||||||
is.clear();
|
is.clear();
|
||||||
|
|||||||
@ -71,11 +71,9 @@ colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp,
|
|||||||
_random = new LAMMPS_NS::RanPark(lmp,seed);
|
_random = new LAMMPS_NS::RanPark(lmp,seed);
|
||||||
|
|
||||||
first_timestep=true;
|
first_timestep=true;
|
||||||
total_force_requested=false;
|
|
||||||
previous_step=-1;
|
previous_step=-1;
|
||||||
t_target=temp;
|
t_target=temp;
|
||||||
do_exit=false;
|
do_exit=false;
|
||||||
restart_every=0;
|
|
||||||
|
|
||||||
// User-scripted forces are not available in LAMMPS
|
// User-scripted forces are not available in LAMMPS
|
||||||
force_script_defined = false;
|
force_script_defined = false;
|
||||||
@ -94,15 +92,17 @@ colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp,
|
|||||||
|
|
||||||
// check if it is possible to save output configuration
|
// check if it is possible to save output configuration
|
||||||
if ((!output_prefix_str.size()) && (!restart_output_prefix_str.size())) {
|
if ((!output_prefix_str.size()) && (!restart_output_prefix_str.size())) {
|
||||||
fatal_error("Error: neither the final output state file or "
|
error("Error: neither the final output state file or "
|
||||||
"the output restart file could be defined, exiting.\n");
|
"the output restart file could be defined, exiting.\n");
|
||||||
}
|
}
|
||||||
|
|
||||||
// try to extract a restart prefix from a potential restart command.
|
// try to extract a restart prefix from a potential restart command.
|
||||||
LAMMPS_NS::Output *outp = _lmp->output;
|
LAMMPS_NS::Output *outp = _lmp->output;
|
||||||
if ((outp->restart_every_single > 0) && (outp->restart1 != 0)) {
|
if ((outp->restart_every_single > 0) && (outp->restart1 != 0)) {
|
||||||
|
restart_frequency_engine = outp->restart_every_single;
|
||||||
restart_output_prefix_str = std::string(outp->restart1);
|
restart_output_prefix_str = std::string(outp->restart1);
|
||||||
} else if ((outp->restart_every_double > 0) && (outp->restart2a != 0)) {
|
} else if ((outp->restart_every_double > 0) && (outp->restart2a != 0)) {
|
||||||
|
restart_frequency_engine = outp->restart_every_double;
|
||||||
restart_output_prefix_str = std::string(outp->restart2a);
|
restart_output_prefix_str = std::string(outp->restart2a);
|
||||||
}
|
}
|
||||||
// trim off unwanted stuff from the restart prefix
|
// trim off unwanted stuff from the restart prefix
|
||||||
@ -207,12 +207,18 @@ double colvarproxy_lammps::compute()
|
|||||||
first_timestep = false;
|
first_timestep = false;
|
||||||
} else {
|
} else {
|
||||||
// Use the time step number from LAMMPS Update object
|
// Use the time step number from LAMMPS Update object
|
||||||
if ( _lmp->update->ntimestep - previous_step == 1 )
|
if ( _lmp->update->ntimestep - previous_step == 1 ) {
|
||||||
colvars->it++;
|
colvars->it++;
|
||||||
// Other cases could mean:
|
b_simulation_continuing = false;
|
||||||
|
} else {
|
||||||
|
// Cases covered by this condition:
|
||||||
// - run 0
|
// - run 0
|
||||||
// - beginning of a new run statement
|
// - beginning of a new run statement
|
||||||
// then the internal counter should not be incremented
|
// The internal counter is not incremented, and the objects are made
|
||||||
|
// aware of this via the following flag
|
||||||
|
b_simulation_continuing = true;
|
||||||
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
previous_step = _lmp->update->ntimestep;
|
previous_step = _lmp->update->ntimestep;
|
||||||
|
|
||||||
@ -275,13 +281,6 @@ void colvarproxy_lammps::serialize_status(std::string &rst)
|
|||||||
rst = os.str();
|
rst = os.str();
|
||||||
}
|
}
|
||||||
|
|
||||||
void colvarproxy_lammps::write_output_files()
|
|
||||||
{
|
|
||||||
// TODO skip output if undefined
|
|
||||||
colvars->write_restart_file(cvm::output_prefix()+".colvars.state");
|
|
||||||
colvars->write_output_files();
|
|
||||||
}
|
|
||||||
|
|
||||||
// set status from string
|
// set status from string
|
||||||
bool colvarproxy_lammps::deserialize_status(std::string &rst)
|
bool colvarproxy_lammps::deserialize_status(std::string &rst)
|
||||||
{
|
{
|
||||||
@ -322,13 +321,6 @@ void colvarproxy_lammps::log(std::string const &message)
|
|||||||
|
|
||||||
|
|
||||||
void colvarproxy_lammps::error(std::string const &message)
|
void colvarproxy_lammps::error(std::string const &message)
|
||||||
{
|
|
||||||
// In LAMMPS, all errors are fatal
|
|
||||||
fatal_error(message);
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
void colvarproxy_lammps::fatal_error(std::string const &message)
|
|
||||||
{
|
{
|
||||||
log(message);
|
log(message);
|
||||||
_lmp->error->one(FLERR,
|
_lmp->error->one(FLERR,
|
||||||
|
|||||||
@ -41,11 +41,9 @@ class colvarproxy_lammps : public colvarproxy {
|
|||||||
// state of LAMMPS properties
|
// state of LAMMPS properties
|
||||||
double t_target, my_timestep, my_boltzmann, my_angstrom;
|
double t_target, my_timestep, my_boltzmann, my_angstrom;
|
||||||
double bias_energy;
|
double bias_energy;
|
||||||
int restart_every;
|
|
||||||
int previous_step;
|
int previous_step;
|
||||||
|
|
||||||
bool first_timestep;
|
bool first_timestep;
|
||||||
bool total_force_requested;
|
|
||||||
bool do_exit;
|
bool do_exit;
|
||||||
|
|
||||||
std::vector<int> atoms_types;
|
std::vector<int> atoms_types;
|
||||||
@ -59,7 +57,7 @@ class colvarproxy_lammps : public colvarproxy {
|
|||||||
const char *, const int, const double, MPI_Comm);
|
const char *, const int, const double, MPI_Comm);
|
||||||
virtual ~colvarproxy_lammps();
|
virtual ~colvarproxy_lammps();
|
||||||
void init(const char*);
|
void init(const char*);
|
||||||
int setup();
|
virtual int setup();
|
||||||
|
|
||||||
// disable default and copy constructor
|
// disable default and copy constructor
|
||||||
private:
|
private:
|
||||||
@ -82,9 +80,6 @@ class colvarproxy_lammps : public colvarproxy {
|
|||||||
// set status from string
|
// set status from string
|
||||||
bool deserialize_status(std::string &);
|
bool deserialize_status(std::string &);
|
||||||
|
|
||||||
// Write files expected from Colvars (called by post_run())
|
|
||||||
void write_output_files();
|
|
||||||
|
|
||||||
// read additional config from file
|
// read additional config from file
|
||||||
int add_config_file(char const *config_filename);
|
int add_config_file(char const *config_filename);
|
||||||
|
|
||||||
@ -103,14 +98,11 @@ class colvarproxy_lammps : public colvarproxy {
|
|||||||
inline cvm::real temperature() { return t_target; };
|
inline cvm::real temperature() { return t_target; };
|
||||||
inline cvm::real dt() { return my_timestep; }; // return _lmp->update->dt * _lmp->force->femtosecond; };
|
inline cvm::real dt() { return my_timestep; }; // return _lmp->update->dt * _lmp->force->femtosecond; };
|
||||||
|
|
||||||
inline size_t restart_frequency() { return restart_every; };
|
|
||||||
|
|
||||||
void add_energy(cvm::real energy) { bias_energy += energy; };
|
void add_energy(cvm::real energy) { bias_energy += energy; };
|
||||||
void request_total_force(bool yesno) { total_force_requested = yesno; };
|
void request_total_force(bool yesno) { total_force_requested = yesno; };
|
||||||
|
|
||||||
void log(std::string const &message);
|
void log(std::string const &message);
|
||||||
void error(std::string const &message);
|
void error(std::string const &message);
|
||||||
void fatal_error(std::string const &message);
|
|
||||||
|
|
||||||
cvm::rvector position_distance(cvm::atom_pos const &pos1,
|
cvm::rvector position_distance(cvm::atom_pos const &pos1,
|
||||||
cvm::atom_pos const &pos2) const;
|
cvm::atom_pos const &pos2) const;
|
||||||
|
|||||||
@ -1,3 +1,3 @@
|
|||||||
#ifndef COLVARPROXY_VERSION
|
#ifndef COLVARPROXY_VERSION
|
||||||
#define COLVARPROXY_VERSION "2019-12-04"
|
#define COLVARPROXY_VERSION "2020-04-07"
|
||||||
#endif
|
#endif
|
||||||
|
|||||||
@ -499,7 +499,7 @@ int FixColvars::modify_param(int narg, char **arg)
|
|||||||
if (me == 0) {
|
if (me == 0) {
|
||||||
if (! proxy)
|
if (! proxy)
|
||||||
error->one(FLERR,"Cannot use fix_modify before initialization");
|
error->one(FLERR,"Cannot use fix_modify before initialization");
|
||||||
return proxy->add_config_file(arg[1]) == COLVARS_OK ? 0 : 2;
|
return proxy->add_config_file(arg[1]) == COLVARS_OK ? 2 : 0;
|
||||||
}
|
}
|
||||||
return 2;
|
return 2;
|
||||||
} else if (strcmp(arg[0],"config") == 0) {
|
} else if (strcmp(arg[0],"config") == 0) {
|
||||||
@ -508,7 +508,7 @@ int FixColvars::modify_param(int narg, char **arg)
|
|||||||
if (! proxy)
|
if (! proxy)
|
||||||
error->one(FLERR,"Cannot use fix_modify before initialization");
|
error->one(FLERR,"Cannot use fix_modify before initialization");
|
||||||
std::string const conf(arg[1]);
|
std::string const conf(arg[1]);
|
||||||
return proxy->add_config_string(conf) == COLVARS_OK ? 0 : 2;
|
return proxy->add_config_string(conf) == COLVARS_OK ? 2 : 0;
|
||||||
}
|
}
|
||||||
return 2;
|
return 2;
|
||||||
} else if (strcmp(arg[0],"load") == 0) {
|
} else if (strcmp(arg[0],"load") == 0) {
|
||||||
@ -516,7 +516,7 @@ int FixColvars::modify_param(int narg, char **arg)
|
|||||||
if (me == 0) {
|
if (me == 0) {
|
||||||
if (! proxy)
|
if (! proxy)
|
||||||
error->one(FLERR,"Cannot use fix_modify before initialization");
|
error->one(FLERR,"Cannot use fix_modify before initialization");
|
||||||
return proxy->read_state_file(arg[1]) == COLVARS_OK ? 0 : 2;
|
return proxy->read_state_file(arg[1]) == COLVARS_OK ? 2 : 0;
|
||||||
}
|
}
|
||||||
return 2;
|
return 2;
|
||||||
}
|
}
|
||||||
@ -984,7 +984,7 @@ void FixColvars::restart(char *buf)
|
|||||||
void FixColvars::post_run()
|
void FixColvars::post_run()
|
||||||
{
|
{
|
||||||
if (me == 0) {
|
if (me == 0) {
|
||||||
proxy->write_output_files();
|
proxy->post_run();
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
Reference in New Issue
Block a user